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1

SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA  

Microsoft Academic Search

SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a

MICHAEL KIPP; FRANK GOHRING; THORSTEN OSTENDORP; Drunen van C. M; ROEL VAN DRIEL; MICHAEL PRZYBYLSKI; F. O. Fackelmaer

2000-01-01

2

A DNA Region Recognized by the Nitric Oxide-Responsive Transcriptional Activator NorR Is Conserved in ?- and ?-Proteobacteria  

PubMed Central

The ?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-(N7)-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-(N7)-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).

Busch, Andrea; Pohlmann, Anne; Friedrich, Barbel; Cramm, Rainer

2004-01-01

3

Inability to induce consistent T-cell responses recognizing conserved regions within HIIV-1 antigens: a potential mechanism for lack of vaccine efficacy in the step study  

SciTech Connect

T cell based vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a high probability of matching the epitope induced by vaccination with the infecting viral strain. We compared the frequency and specificity of the CTL epitopes elicited by the replication defective AdS gag/pol/nef vaccine used in the STEP trial with the likelihood of encountering those epitopes among recently sequenced Clade B isolates of HIV-1. On average vaccination elicited only one epitope per gene. Importantly, the highly conserved epitopes in gag, pol, and nef (> 80% of strains in the current collection of the Los Alamos database [www.hiv.lanl.gov]) were rarely elicited by vaccination. Moreover there was a statistically significant skewing of the T cell response to relative variable epitopes of each gene; only 20% of persons possessed > 3 T cell responses to epitopes likely to be found in circulating strains in the CladeB populations in which the Step trial was conducted. This inability to elicit T cell responses likely to be found in circulating viral strains is a likely factor in the lack of efficacy of the vaccine utilized in the STEP trial. Modeling of the epitope specific responses elicited by vaccination, we project that a median of 8-10 CD8+ T cell epitopes are required to provide >80% likelihood of eliciting at least 3 CD8+ T cell epitopes that would be found on a circulating population of viruses. Development of vaccine regimens which elicit either a greater breadth of responses or elicit responses to conserved regions of the HIV-1 genome are needed to fully evaluate the concept of whether induction of T cell immunity can alter HIV-1 in vivo.

Korber, Bette [Los Alamos National Laboratory; Szinger, James [Los Alamos National Laboratory

2009-01-01

4

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

5

Monoclonal antibodies PG-B6a and PG-B6p recognize, respectively, a highly conserved and a formol-resistant epitope on the human BCL-6 protein amino-terminal region.  

PubMed Central

The human BCL-6 gene, which is rearranged in approximately 30% of diffuse large B cell lymphomas, encodes a 706-amino-acid nuclear protein of the Kruppel-type zinc finger transcription factors mainly expressed in normal germinal center B cells and related lymphomas. Four monoclonal antibodies (PG-B6, PG-B6a, PG-B6p, and PG-B6m), specifically directed against the human BCL-6 protein, were generated by immunizing BALB/c mice with a recombinant protein corresponding to the BCL-6 amino-terminal region (amino acids 3 to 484). The PG-B6 monoclonal antibody reacted with a BCL-6 epitope sensitive to fixatives and preserved in all mammalian species. PG-B6a (a is for avian) recognized the most evolutionarily conserved BCL-6 epitope (expressed in all animal species including avian). PG-B6p (p is for paraffin) recognized a fixative-resistant epitope of BCL-6 that was detectable on paraffin sections after microwave heating in 1 mmol/L EDTA buffer. PG-B6m (m is for mantle) was the least specific monoclonal antibody as, in addition to BCL-6, it reacted with a yet undefined antigen selectively located in the cytoplasm of mantle and marginal zone B cells. All monoclonal antibodies detected strong nuclear expression of BCL-6 in follicular lymphomas, diffuse large B cell lymphomas, Burkitt's lymphomas, and nodular, lymphocyte-predominance Hodgkin's disease. In diffuse large B cell lymphomas, BCL-6 expression was independent of BCL-6 gene rearrangements and did not correlate with expression of other markers or the proliferation index. BCL-6 was not expressed in B-CLL, hairy cell leukemia, mantle-cell- and marginal-zone-derived lymphomas. Labeling of paraffin sections with PG-B6p proved useful for differentiating proliferation centers in B-CLL (BCl-2+/BCL-6-) from trapped germinal centers in mantle cell lymphomas (BCL-2-/BCL-6+) and for identifying neoplastic cells in cases of nodular, lymphocyte-predominance Hodgkin's disease. Because of their high specificity, wide reactivity in humans and animal species including avians (PG-B6a), and suitability for labeling routine paraffin sections (PG-B6p), the reagents described in this paper should prove valuable in both research and diagnostics. Images Figure 2 Figure 1 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7

Flenghi, L.; Bigerna, B.; Fizzotti, M.; Venturi, S.; Pasqualucci, L.; Pileri, S.; Ye, B. H.; Gambacorta, M.; Pacini, R.; Baroni, C. D.; Pescarmona, E.; Anagnostopoulos, I.; Stein, H.; Asdrubali, G.; Martelli, M. F.; Pelicci, P. G.; Dalla-Favera, R.; Falini, B.

1996-01-01

6

Human immunodeficiency virus neutralizing antibodies recognize several conserved domains on the envelope glycoproteins.  

PubMed Central

Serum neutralizing antibodies against the human immunodeficiency virus were frequently detected in infected individuals, and low or absent serum neutralizing titers correlated with poor prognosis. Multiple diverse human immunodeficiency virus isolates were found to exhibit similar susceptibility to neutralization by a panel of human seropositive sera, suggesting that neutralizing antibodies are largely directed against conserved viral domains. Furthermore, utilizing antisera raised against a library of synthetic env peptides, four regions which are important in the neutralization process have been identified within both human immunodeficiency virus envelope glycoproteins (gp41 and gp120). Three of these are in conserved domains and should be considered for inclusion in a candidate vaccine. Images

Ho, D D; Sarngadharan, M G; Hirsch, M S; Schooley, R T; Rota, T R; Kennedy, R C; Chanh, T C; Sato, V L

1987-01-01

7

Monoclonal Antibodies with Broad Specificity for Hepatitis C Virus Hypervariable Region 1 Variants Can Recognize Viral Particles1  

Microsoft Academic Search

The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is a highly heterogeneous sequence that is promiscuously recognized by human sera via binding to amino acid residues with conserved physicochemical properties. We generated a panel of mAbs from mice immunized with HVR1 surrogate peptides (mimotopes) affinity-selected with sera from HCV-infected patients from a phage display

Antonella Cerino; Annalisa Meola; Laura Segagni; Milena Furione; Sabrina Marciano; Miriam Triyatni; T. Jake Liang; Alfredo Nicosia; Mario U. Mondelli

2001-01-01

8

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

Code of Federal Regulations, 2011 CFR

...federally recognized Indian tribes or Alaska Native villages or regional or village...federally recognized Indian tribes or Alaska Native villages or regional or village corporations. (a) Tribal or Alaska Native gifts. In addition...

2013-01-01

9

Conservative management of regional odontodysplasia: case report.  

PubMed

Regional odontodysplasia is an uncommon developmental anomaly affecting a localized area of the dentition. The affected teeth are often grossly malformed and develop abscess soon after eruption. Although extractions are often required, in some milder cases the teeth may be retained for a long period. The treatment plan should be based on the degree of involvement as well as functional and esthetic needs in each case. This article describes a conservative treatment approach in a 10-year-old boy with regional odontodysplasia. PMID:17049109

Cho, Shiu-yin

2006-10-01

10

Promoter regions of Plasmodium vivax are poorly or not recognized by Plasmodium falciparum  

Microsoft Academic Search

BACKGROUND: Heterologous promoter analysis in Plasmodium has revealed the existence of conserved cis regulatory elements as promoters from different species can drive expression of reporter genes in heterologous transfection assays. Here, the functional characterization of different Plasmodium vivax promoters in Plasmodium falciparum using luciferase as the reporter gene is presented. METHODS: Luciferase reporter plasmids harboring the upstream regions of the

Mauro F Azevedo; Hernando A del Portillo

2007-01-01

11

A CACGTG Motif of the Antirrhinum majus Chalcone Synthase Promoter is Recognized by an Evolutionarily Conserved Nuclear Protein  

Microsoft Academic Search

In the chalcone synthase gene of Antirrhinum majus (snapdragon), 150 base pairs of the 5' flanking region contain cis-acting signals for UV light-induced expression. A nuclear factor, designated CG-1, specifically recognizes a hexameric motif with internal dyad symmetry, CACGTG, located within this light-responsive sequence. Binding of CG-1 is influenced by C-methylation of the CpG dinucleotide in the recognition sequence. CG-1

Dorothee Staiger; Hildegard Kaulen; Jeff Schell

1989-01-01

12

Identification and Characterization of a Conserved, Stage-Specific Gene Product of Plasmodium falciparum Recognized by Parasite Growth Inhibitory Antibodies  

Microsoft Academic Search

We have identified a novel conserved protein of Plasmodium falciparum, designated D13, that is stage- specifically expressed in asexual blood stages of the parasite. The predicted open reading frame (ORF) D13 contains 863 amino acids with a calculated molecular mass of 99.7 kDa and displays a repeat region composed of pentapeptide motives. Northern blot analysis with lysates of synchronized blood

Claudia A. Daubenberger; Diana Diaz; Marija Curcic; Markus S. Mueller; Tobias Spielmann; Ulrich Certa; Joachim Lipp; G. Pluschke

2003-01-01

13

Species distributions, surrogacy, and important conservation regions in Canada  

Microsoft Academic Search

Conservation actions could be more efficient if there is congruence among taxa in the distribution of species. Patterns in the geographical distribution of five taxa were used to identify nationally important regions for conservation in Canada. Two measures of surrogacy were significantly and positively correlated among taxa, and conservation areas selected for one taxon represented other taxa significantly better than

Leanna D. Warman; David M. Forsyth; A. R. E. Sinclair; Kathryn Freemark; Harold D. Moore; Thomas W. Barrett; R. L. Pressey; Denis White

2004-01-01

14

PCR Use of Highly Conserved DNA Regions for Identification of Sinorhizobium meliloti  

PubMed Central

A PCR identification method in which four primers that recognize homologous conserved regions in the Sinorhizobium meliloti genome are used was developed and tested. The regions used for identification were the nodbox 4 locus, which is located in one of the symbiotic megaplasmids, and the mucR gene, which is located in the chromosome. The new method was used to establish a collection of S. meliloti strains from polluted soils.

Sanchez-Contreras, Maria; Lloret, Javier; Martin, Marta; Villacieros, Marta; Bonilla, Ildefonso; Rivilla, Rafael

2000-01-01

15

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

16

Epitope mapping reveals conserved regions of an auxin-binding protein.  

PubMed Central

There is now good evidence that maize (Zea mays) auxin-binding protein (ABP) functions as a receptor. We have synthesized sequential overlapping hexapeptides to map the epitopes recognized by a number of antisera to ABP. Only a few regions of the protein are recognized, and these are shown to be exposed on the surface. Three epitopes predominate, and these are clustered around, but do not include, the glycosylation site. A comparison is made between these maps of sera against purified ABP, maps of sera raised against recombinant maize ABP expressed in Escherichia coli and computer antigenicity predictions. Our anti-(maize ABP) serum recognizes ABP counterparts in other plant species. We have used immunoblotting to affinity-purify the immunoglobulins which cross-react from the antiserum. Epitope mapping of these immunoglobulins suggests that two of the three predominant epitopes may be conserved in both monocotyledonous and dicotyledonous plants. The possible functional significance of these conserved epitopes is discussed. Images Fig. 4.

Napier, R M; Venis, M A

1992-01-01

17

Epitope mapping reveals conserved regions of an auxin-binding protein.  

PubMed

There is now good evidence that maize (Zea mays) auxin-binding protein (ABP) functions as a receptor. We have synthesized sequential overlapping hexapeptides to map the epitopes recognized by a number of antisera to ABP. Only a few regions of the protein are recognized, and these are shown to be exposed on the surface. Three epitopes predominate, and these are clustered around, but do not include, the glycosylation site. A comparison is made between these maps of sera against purified ABP, maps of sera raised against recombinant maize ABP expressed in Escherichia coli and computer antigenicity predictions. Our anti-(maize ABP) serum recognizes ABP counterparts in other plant species. We have used immunoblotting to affinity-purify the immunoglobulins which cross-react from the antiserum. Epitope mapping of these immunoglobulins suggests that two of the three predominant epitopes may be conserved in both monocotyledonous and dicotyledonous plants. The possible functional significance of these conserved epitopes is discussed. PMID:1377914

Napier, R M; Venis, M A

1992-06-15

18

The Structure of the Staphylococcus aureus Sortase-Substrate Complex Reveals How the Universally Conserved LPXTG Sorting Signal Is Recognized*  

PubMed Central

In Gram-positive bacteria, sortase enzymes assemble surface proteins and pili in the cell wall envelope. Sortases catalyze a transpeptidation reaction that joins a highly conserved LPXTG sorting signal within their polypeptide substrate to the cell wall or to other pilin subunits. The molecular basis of transpeptidation and sorting signal recognition are not well understood, because the intermediates of catalysis are short lived. We have overcome this problem by synthesizing an analog of the LPXTG signal whose stable covalent complex with the enzyme mimics a key thioacyl catalytic intermediate. Here we report the solution structure and dynamics of its covalent complex with the Staphylococcus aureus SrtA sortase. In marked contrast to a previously reported crystal structure, we show that SrtA adaptively recognizes the LPXTG sorting signal by closing and immobilizing an active site loop. We have also used chemical shift mapping experiments to localize the binding site for the triglycine portion of lipid II, the second substrate to which surface proteins are attached. We propose a unified model of the transpeptidation reaction that explains the functions of key active site residues. Since the sortase-catalyzed anchoring reaction is required for the virulence of a number of bacterial pathogens, the results presented here may facilitate the development of new anti-infective agents.

Suree, Nuttee; Liew, Chu Kong; Villareal, Valerie A.; Thieu, William; Fadeev, Evgeny A.; Clemens, Jeremy J.; Jung, Michael E.; Clubb, Robert T.

2009-01-01

19

Suitability for conservation as a criterion in regional conservation network selection  

Microsoft Academic Search

The process of selecting candidate areas for inclusion in a regional conservation network should include not only delineating\\u000a appropriate land units for selection and defining targets for representing features of interest, but also determining the\\u000a suitability of land units for conservation purposes. We developed an explicit rating of conservation suitability by applying\\u000a fuzzy-logic functions in a knowledge base to ecological

Hope C. Humphries; Patrick S. Bourgeron; Keith M. Reynolds

2008-01-01

20

Setting priorities for regional conservation planning in the Mediterranean Sea.  

PubMed

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. PMID:23577060

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

2013-04-05

21

Conservation of epitopes recognized by monoclonal antibodies against the separated subunits of influenza hemagglutinin among type A viruses of the same and different subtypes  

Microsoft Academic Search

Summary Monoclonal antibodies raised against the separated hemagglutinin subunits (HA1 and HA2) of influenza A\\/Vic\\/3\\/75 (H3N2) virus were tested against a large panel of human and avian strains. The epitopes recognized by most antibodies were conserved among subtype H3 viruses, but reactivity of some antibodies with members of other subtypes was also observed. Particularly, the H4 virus reacted with most

Alicia Sanchez-Fauquier; Matilde Guillen; J. Martin; A. P. Kendal; J. A. Melero

1991-01-01

22

Phylogenetic conservation of a snake venom metalloproteinase epitope recognized by a monoclonal antibody that neutralizes hemorrhagic activity.  

PubMed

Snake venom metalloproteinases (SVMPs) are present in large quantities in venoms of viper snakes and also in some elapids. Jararhagin is a representative of a P-III multidomain hemorrhagic SVMP present in Bothrops jararaca venom. It is comprised of a catalytic, a disintegrin-like and a cysteine-rich domain. Seven anti-jararhagin monoclonal antibodies (MAJar 1-7) were produced, of which six reacted with the disintegrin domain. MAJar 3 recognized an epitope present at the C-terminal part of the disintegrin-like domain, and neutralized jararhagin-induced hemorrhage. In this study, we evaluated the reactivity of these monoclonal antibodies with venoms from 27 species of snakes belonging to different families. MAJar 3 recognized most of the hemorrhagic venoms. By ELISA, MAJar 3 reacted strongly with venoms from Viperidae family and weakly with Colubridae and Elapidae venoms. This recognition pattern was due to bands between 50 and 80 kDa, corresponding to P-III SVMPs. This antibody preferentially neutralized the hemorrhage induced by venoms of Bothrops snakes. This fact suggests that the epitope recognized by MAJar 3 is present in other metalloproteinases throughout snake phylogeny. However, slight structural differences in the epitope may result in insufficient affinity for neutralization of biological activities. PMID:14757213

Tanjoni, Isabelle; Butera, Diego; Spencer, Patrick J; Takehara, Harumi A; Fernandes, Irene; Moura-da-Silva, Ana Maria

2003-12-01

23

Production of monoclonal antibody, PR81, recognizing the tandem repeat region of MUC1 mucin.  

PubMed

A monoclonal antibody (MAb) was generated by immunizing BALB/c mice with homogenized breast cancerous tissues. This antibody (PR81) was found to be of IgG(1) class and subclass, containing kappa light chain. PR81 reacted with either the membrane extracts of several breast cancerous tissues or the cell surface of some MUC1 positive cell lines (MCF-7, BT-20 and T-47D) tested by enzyme immunoassay and for MCF-7 by immunofluorescence method. PR81 also reacted with two synthetic 27 and 16-amino acid peptides, TSA-P1-24 and A-P1-15, respectively, which included the core tandem repeat sequence of MUC1. However, this antibody did not react with a synthetic 14 amino acid peptide that has no similarity with tandem repeat found in MUC1. The generated antibody had good and similar affinities (2.19 x 10(8) M(-1)) toward TSA-P1-24 and A-P1-15, which are mainly shared in the hydrophilic sequence of PDTRPAP. Through Western blot analysis of homogenized breast tissues, PR81 recognized only a major band of 250 kDa. This band is stronger in malignant tissue than benign and normal tissues. PMID:12954100

Paknejad, M; Rasaee, M J; Tehrani, F Karami; Kashanian, S; Mohagheghi, M A; Omidfar, K; Bazl, M Rajabi

2003-06-01

24

Do young women in tropical regions constitute a recognized social category?  

Microsoft Academic Search

In most tropical regions is little organized health care for young women, yet their household roles within contexts of worsening socio-economic situations create special health problems. In the area of sexual and reproductive health, the onset of reproductive roles does not entitle the young women to either maternal and child health services or family planning services unless they are married

Beth Maina Ahlberg

1996-01-01

25

The importance of birds for conservation in the Neotropical region  

Microsoft Academic Search

Habitat loss remains the major threat to birds in the Neotropics, although there are several additional specific threats,\\u000a for example trade, nest parasitism, invasives on islands, and for seabirds, bycatch. Capacity building also remains a key\\u000a issue for conservation in the area. Nevertheless, the region has benefited by a surge in research, with an increase in Neotropical\\u000a avian studies over

Jaime García-Moreno; Rob P. Clay; César A. Ríos-Muńoz

2007-01-01

26

Regional odontodysplasia: an unusual case with a conservative approach.  

PubMed

A case of a 14-year-old male with regional odontodysplasia is reported. In this presentation many atypical clinical and radiographical features of this condition are present. The chief complaint of the patient was the enlargement of the gingiva and, according to the literature, inflammatory processes are the main reason why patients look for care. Moreover, there was no radiographic evidence of unerupted teeth in this report. The functional and psychological benefits of the conservative approach are emphasised. PMID:10379086

Marques, A C; Castro, W H; do Carmo, M A

1999-05-22

27

Definition of epitopes and antigens recognized by vaccinia specific immune responses: Their conservation in variola virus sequences, and use as a model system to study complex pathogens  

PubMed Central

In the last few years, a wealth of information has become available relating to the targets of vaccinia virus (VACV)-specific CD4+ T cell, CD8+ T cell and antibody responses. Due to the large size of its genome, encoding more than 200 different proteins, VACV represents a useful model system to study immunity to complex pathogens. Our data demonstrate that both cellular and humoral responses target a large number of antigens and epitopes. This broad spectrum of targets is detected in both mice and humans. CD4+ T cell responses target late and structural antigens, while CD8+ T cells preferentially recognize early antigens. While both CD4+ and CD8+ T cell responses target different types of antigens, the antigens recognized by TH cells are highly correlated with those recognized by antibody responses. We further show that protein abundance and antibody recognition can be used to predict antigens recognized by CD4+ T cell responses, while early expression at the mRNA level predicts antigens targeted by CD8+ T cells. Finally, we find that the vast majority of VACV epitopes are conserved in variola virus (VARV), thus suggesting that the epitopes defined herein also have relevance for the efficacy of VACV as a smallpox vaccine.

Sette, Alessandro; Grey, Howard; Oseroff, Carla; Peters, Bjoern; Moutaftsi, Magdalini; Crotty, Shane; Assarsson, Erika; Greenbaum, Jay; Kim, Yohan; Kolla, Ravi; Tscharke, David; Koelle, David; Johnson, R. Paul; Blum, Janice; Head, Steven; Sidney, John

2010-01-01

28

Conservation of Regional Gene Expression in Mouse and Human Brain  

PubMed Central

Many neurodegenerative diseases have a hallmark regional and cellular pathology. Gene expression analysis of healthy tissues may provide clues to the differences that distinguish resistant and sensitive tissues and cell types. Comparative analysis of gene expression in healthy mouse and human brain provides a framework to explore the ability of mice to model diseases of the human brain. It may also aid in understanding brain evolution and the basis for higher order cognitive abilities. Here we compare gene expression profiles of human motor cortex, caudate nucleus, and cerebellum to one another and identify genes that are more highly expressed in one region relative to another. We separately perform identical analysis on corresponding brain regions from mice. Within each species, we find that the different brain regions have distinctly different expression profiles. Contrasting between the two species shows that regionally enriched genes in one species are generally regionally enriched genes in the other species. Thus, even when considering thousands of genes, the expression ratios in two regions from one species are significantly correlated with expression ratios in the other species. Finally, genes whose expression is higher in one area of the brain relative to the other areas, in other words genes with patterned expression, tend to have greater conservation of nucleotide sequence than more widely expressed genes. Together these observations suggest that region-specific genes have been conserved in the mammalian brain at both the sequence and gene expression levels. Given the general similarity between patterns of gene expression in healthy human and mouse brains, we believe it is reasonable to expect a high degree of concordance between microarray phenotypes of human neurodegenerative diseases and their mouse models. Finally, these data on very divergent species provide context for studies in more closely related species that address questions such as the origins of cognitive differences.

Strand, Andrew D; Aragaki, Aaron K; Baquet, Zachary C; Hodges, Angela; Cunningham, Philip; Holmans, Peter; Jones, Kevin R; Jones, Lesley; Kooperberg, Charles; Olson, James M

2007-01-01

29

Regional nodal irradiation in the conservative treatment of breast cancer  

SciTech Connect

At this institution conservative treatment of breast cancer was begun in the 1960's. The following analysis represents our experience through 1984 with specific reference to the management of the regional lymph nodes. A total of 432 patients with clinical stage I and II breast cancer were treated between 1962 and 1984 with lumpectomy and radiation therapy. The breast was treated with tangential fields to a median dose of 4800 cGy and electron conedown to a total tumor bed dose of 6400 cGy. Axillary dissection was not routinely performed, particularly in the earlier years. More recently, axillary dissection has been used with increasing frequency if it was felt that the results of the dissection would influence systemic treatment. One hundred eighty-seven patients (43%) underwent axillary dissection and routinely received regional nodal irradiation to the internal mammary and supraclavicular lymph nodes. Two hundred forty-five patients (57%) did not undergo axillary dissection and routinely received regional nodal irradiation to the internal mammary, supraclavicular, and entire axillary regions to a total median dose of 4600 cGy. As of May 1989 with a median follow-up of 7.5 years, there have been a total of 12 nodal failures for an actuarial nodal control rate of 97% at 5 years and 96% at 10 years. The actuarial 5-year regional nodal control rate was the same for both the group of patients receiving regional RT alone without axillary dissection and the group of patients receiving axillary dissection and supraclavicular/internal mammary radiation. There has been minimal morbidity associated with this treatment policy. We conclude that regional nodal irradiation, with or without axillary dissection, results in a high rate of regional nodal control and minimal treatment morbidity in patients undergoing conservative treatment of early stage breast cancer.

Haffty, B.G.; Fischer, D.; Fischer, J.J. (Yale Univ. School of Medicine, New Haven, CT (USA))

1990-10-01

30

Conservation planning at the landscape scale: A landscape ecology method for regional land trusts  

Microsoft Academic Search

This paper illustrates a landscape ecology approach for land trusts undertaking conservation at the watershed scale. A conservation plan was created for the Grand Traverse Regional Land Conservancy (GTRLC) in the headwaters of Michigan's Manistee River Watershed (USA). Eight conservation drivers were devised to identify Conservation Focus Areas (CFAs) of highest ecological importance. The CFAs were ranked based on ecological

Jonathan Kazmierski; Megan Kram; Elizabeth Mills; David Phemister; Nicholas Reo; Christopher Riggs; Ryan Tefertiller; Donna Erickson

2004-01-01

31

Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.  

PubMed

Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis phages SPR and phi 3T methylate the internal cytosine of the sequence GGCC. They differ in their capacity to methylate additional sequences. These are CCGG and CC(A/T)GG in SPR and GCNGC in phi 3T. Introducing unique restriction sites at equivalent locations within the two genes facilitated the construction of chimeric genes. These expressed Mtase activity at a level comparable to that of the parental genes. The methylation specificity of chimeric enzymes was correlated with the location of chimeric fusions. This analysis, which also included the use of mutant genes, showed that domains involved in the recognition of target sequences unique to each enzyme [CCGG, CC(A/T)GG or GCNGC] are represented by the central non-conserved parts of the proteins, whilst recognition of the sequence (GGCC), which is a target for both enzymes, is determined by an adjacent conserved region. PMID:2828032

Balganesh, T S; Reiners, L; Lauster, R; Noyer-Weidner, M; Wilke, K; Trautner, T A

1987-11-01

32

Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.  

PubMed Central

Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis phages SPR and phi 3T methylate the internal cytosine of the sequence GGCC. They differ in their capacity to methylate additional sequences. These are CCGG and CC(A/T)GG in SPR and GCNGC in phi 3T. Introducing unique restriction sites at equivalent locations within the two genes facilitated the construction of chimeric genes. These expressed Mtase activity at a level comparable to that of the parental genes. The methylation specificity of chimeric enzymes was correlated with the location of chimeric fusions. This analysis, which also included the use of mutant genes, showed that domains involved in the recognition of target sequences unique to each enzyme [CCGG, CC(A/T)GG or GCNGC] are represented by the central non-conserved parts of the proteins, whilst recognition of the sequence (GGCC), which is a target for both enzymes, is determined by an adjacent conserved region. Images Fig. 4. Fig. 5.

Balganesh, T S; Reiners, L; Lauster, R; Noyer-Weidner, M; Wilke, K; Trautner, T A

1987-01-01

33

cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera  

SciTech Connect

The authors have isolated a 1.1-kilobase cDNA clone that encodes human fibrillarin by screening a hepatoma library in parallel with DNA probes derived from the fibrillarin genes of Saccharomyces cerevisiae (NOP1) and Xenopus laevis. RNA blot analysis indicates that the corresponding mRNA is {approximately}1,300 nucleotides in length. Human fibrillarin expressed in vitro migrates on SDS gels as a 36-kDa protein that is specifically immunoprecipitated by antisera from humans with scleroderma autoimmune disease. Human fibrillarin contains an amino-terminal repetitive domain {approximately}75-80 amino acids in length that is rich in glycine and arginine residues and is similar to amino-terminal domains in the yeast and Xenopus fibrillarins. The occurrence of a putative RNA-binding domain and an RNP consensus sequence within the protein is consistent with the association of fibrillarin with small nucleolar RNAs. Protein sequence alignments show that 67% of amino acids from human fibrillarin are identical to those in yeast fibrillarin and that 81% are identical to those in Xenopus fibrillarin. This identity suggests the evolutionary conservation of an important function early in the pathway for ribosome biosynthesis.

Aris, J.P.; Blobel, G. (Rockefeller Univ., New York, NY (United States))

1991-02-01

34

Human Monoclonal Antibodies That Inhibit Binding of Hepatitis C Virus E2 Protein to CD81 and Recognize Conserved Conformational Epitopes  

PubMed Central

The intrinsic variability of hepatitis C virus (HCV) envelope proteins E1 and E2 complicates the identification of protective antibodies. In an attempt to identify antibodies to E2 proteins from divergent HCV isolates, we produced HCV E2 recombinant proteins from individuals infected with HCV genotypes 1a, 1b, 2a, and 2b. These proteins were then used to characterize 10 human monoclonal antibodies (HMAbs) produced from peripheral B cells isolated from an individual infected with HCV genotype 1b. Nine of the antibodies recognize conformational epitopes within HCV E2. Six HMAbs identify epitopes shared among HCV genotypes 1a, 1b, 2a, and 2b. Six, including five broadly reactive HMAbs, could inhibit binding of HCV E2 of genotypes 1a, 1b, 2a, and 2b to human CD81 when E2 and the antibody were simultaneously exposed to CD81. Surprisingly, all of the antibodies that inhibited the binding of E2 to CD81 retained the ability to recognize preformed CD81-E2 complexes generated with some of the same recombinant E2 proteins. Two antibodies that did not recognize preformed complexes of HCV 1a E2 and CD81 also inhibited binding of HCV 1a virions to CD81. Thus, HCV-infected individuals can produce antibodies that recognize conserved conformational epitopes and inhibit the binding of HCV to CD81. The inhibition is mediated via antibody binding to epitopes outside of the CD81 binding site in E2, possibly by preventing conformational changes in E2 that are required for CD81 binding.

Hadlock, Kenneth G.; Lanford, Robert E.; Perkins, Susan; Rowe, Judy; Yang, Qing; Levy, Shoshana; Pileri, Piero; Abrignani, Sergio; Foung, Steven K. H.

2000-01-01

35

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

36

Comprehensive viral oligonucleotide probe design using conserved protein regions  

PubMed Central

Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.

Jabado, Omar J.; Liu, Yang; Conlan, Sean; Quan, P. Lan; Hegyi, Hedi; Lussier, Yves; Briese, Thomas; Palacios, Gustavo; Lipkin, W. I.

2008-01-01

37

Costs and benefits of forest conservation: regional and local comparisons in Eastern Finland  

Microsoft Academic Search

In addition to environmental interests vs. timber production, debates on forest conservation have typically dealt with nationwide vs. local and regional interests. While most previous studies have focused on the nationwide perspective, this paper considers the benefits and costs of existing conservation areas from the regional and local point of view. The non-market benefits of conservation are measured by means

Matleena Kniivilä; Ville Ovaskainen; Olli Saastamoinen

2002-01-01

38

Sp1 Specifically Binds to an Evolutionarily Conserved DNA Segment within a Region Necessary for Podocyte-Specific Expression of Nephrin  

Microsoft Academic Search

We have analyzed a conserved 237-bp segment located in a 1.9-kb upstream region of the nephrin gene, previously shown to contain kidney specific enhancer element(s). Electromobility shift assay was used to identify a 20-nucleotide region specifically recognized and bound by protein factors in nuclear extracts from immortalized podocyte and human embryonic kidney cell lines. The region was further narrowed down

Olga Beltcheva; Eyrun Edda Hjorleifsdottir; Sirpa Kontusaari; Karl Tryggvason

2010-01-01

39

In Vivo Efficacy of a Chimeric Peptide Derived from the Conserved Region of the M Protein against Group C and G Streptococci  

PubMed Central

The J8 peptide from the conserved region of the M protein protects against group A streptococcus infections. In this study, we demonstrate that vaccination with a J8-containing formulation induces IgG that recognizes and binds group C and G streptococci. Moreover, this formulation has the potential to provide protection against infections caused by these organisms.

Nordstrom, Therese; Malcolm, Jessica; Magor, Graham; Good, Michael F.

2012-01-01

40

Recognizing Symptoms  

MedlinePLUS

... My Cart | Register | Sign In Home What Is IBS? Introduction to IBS Facts About IBS Frequently Asked Questions Post-infectious IBS Other Disorders Signs & Symptoms Overview Recognizing Symptoms Pain ...

41

Receptor-recognizing proteins of T-even type bacteriophages. Constant and hypervariable regions and an unusual case of evolution.  

PubMed

Proteins 38 of bacteriophages T2, K3, Ox2 and M1 are located at the free ends of their long tail fibers and function as adhesins, i.e. they mediate binding to the bacterial receptors. The latter three phages use the Escherichia coli outer membrane protein OmpA as a receptor, while T2 uses the outer membrane proteins OmpF or Ttr. The DNA sequences of genes 38 of phages Ox2 and M1 have been determined and are compared with those known for T2 and K3. The genes encode 262(T2), 260(K3), 266(Ox2) and 262(M1) amino acid residues. Three domains are distinguishable in these proteins. There are two conserved regions encompassing about 120 NH2-terminal and about 25 CO2H-terminal residues, respectively. The area between these was found to be hypervariable, and it is shown that a very large number of amino acid substitutions, deletions and/or insertions have occurred. Glycine-rich stretches are present within and flanking these areas. Their positions are essentially conserved, indicating an important structural role in receptor recognition. The hypervariability, most likely caused by a constant struggle with bacterial phage-resistant mutants, is so drastic that one cannot discern that T2 uses different receptors from those of the other phages. The partially known sequence of gene 38 of phage T4 has been completed. The gene encodes a protein consisting of 183 amino acid residues. The amino acid composition and sequence of this protein is completely different from those of phages T2, K3, Ox2 and M1. Also, the protein is functionally unrelated to the other proteins 38: it is not present in phage T4 and, unlike the other proteins 38, is required for the efficient dimerization of protein 37. All phages under study are of the same morphology and the genomic organization of the tail fiber genes is identical, with genes 36, 37 and 38 most likely representing, in this order, a transcriptional unit. Sequence similarities between the CO2H-termini of genes 37 of the non-T4 phages and gene 38 of phage T4 were found; this part of gene 37 does not exist in T4. It is suggested that gene 38 of phage T4 originated from a segment of gene 37 of a T2-type phage. Gene 38 of phage T4 is not unique, DNA-DNA hybridization experiments indicated that two other T-even type phages, TuIa and TuIb, possess a T4-type gene 38. PMID:2958637

Montag, D; Riede, I; Eschbach, M L; Degen, M; Henning, U

1987-07-01

42

Recognizing Energy  

NSDL National Science Digital Library

Energy is such a common notion. We talk about it all the time. Should you buy energy-efficient windows? The country needs an energy policy. That little kid at the store who screaming at the top of his lungs sure has a lot of energy. This chapter deals with recognizing and defining energy. This free selection from Stop Faking It! Finally Understanding Science So You Can Teach It: Energy includes the Table of Contents and Preface.

Robertson, William C.

2002-01-01

43

Determination of national conservation responsibilities for species conservation in regions with multiple political jurisdictions  

Microsoft Academic Search

The Convention on Biodiversity (CBD) commits its signatories to the identification and monitoring of biodiversity. The European\\u000a Union has implemented this commitment into its legislation. Despite the legal requirement resources are scarce, requiring\\u000a a prioritization of conservation actions, including e.g. monitoring. Red lists are currently the most prominent tool for priority\\u000a setting in applied conservation, despite the fact that they

Dirk S. Schmeller; Bernd Gruber; Bianca Bauch; Kaire Lanno; Eduardas Budrys; Valerija Babij; Rimvydas Juškaitis; Marek Sammul; Zoltan Varga; Klaus Henle

2008-01-01

44

Relative occupancy, endemism, taxonomic distinctiveness and vulnerability: prioritizing regional conservation actions  

Microsoft Academic Search

A method is presented whereby regional species are scored and ranked in order of regional conservation importance according to a number of different but complementary 'rarity' criteria. Approaches for determining regional occupancy (RO), relative taxonomic distinctiveness (RTD), relative endemism (RE) and relative vulnerability (RV) rankings for regional faunas are proposed. The continuous variable approach and resultant positively skewed 'rarity' scores

Stefanie Freitag; A. S. Van Jaarsveld

1997-01-01

45

INTEGRATING GRASSLAND AND SHRUBLAND BIRD CONSERVATION WITH THE NORTHERN BOBWHITE CONSERVATION INITIATIVE FOR THE CENTRAL HARDWOODS BIRD CONSERVATION REGION  

Microsoft Academic Search

Much attention has focused on management options to increase Northern Bobwhite (Colinus virginianus) habitat availability including the organization of the Southeast Quail Study Group Technical Committee and the creation of the Northern Bobwhite Conservation Initiative (NBCI). As the NBCI moves from the planning stages to implementation, there is a need to understand how management options for Northern Bobwhite populations will

JAMES J. GIOCOMO; DAVID A. BUEHLER; JANE FITZGERALD

46

[Minimal amino acid sequence, recognized by anibodies to the peptide GPQPPQPPQP from the proline-rich region of pertactin].  

PubMed

Three antiserum samples obtained from rabbits immunized by the conjugate KLH-10P (keyhole limpet hemocyanine-decapeptide GPQPPQPPQP) were used to study antigenic structure of 10P. Antigenic properties of conjugates 6P (PGPQPP) and 4P (PQPP) with ovalbumine were studied by an indirect immunoassay (ELISA). Also 4P, 6P, PQP and QPP peptides were used for a competition assay. It was found that antibodies to 10P have demonstrated different specificity to short sites. Antibodies recognized such shot peptides as PQP and QPP in the competition assay. The efficiency of serum antibodies reaction with those peptides increased from QPP and PQP to PGPQPP. Only one serum sample had no antibodies to glutaraldehyde. Gly-glutaraldehyde-Gly hapten-like ligand was used to inhibit activity of antibodies to cross-linking agent into two samples. It is allowed to improve analysis of antibodies, which recognize shot sequences PQP and QPP. PMID:10726308

Kavun, E M; Kolibo, D V; Romaniuk, S I; Radavski?, Iu L; Komissarenko, S V

47

Functional conservation of the promoter regions of vertebrate tyrosinase genes.  

PubMed

Tyrosinase is the key enzyme for synthesizing melanin pigments, which primarily determine mammalian skin coloration. Considering the important roles of pigments in the evolution and the adaptation of vertebrates, phylogenetic changes in the coding and flanking regulatory sequences of the tyrosinase gene are particularly intriguing. We have now cloned cDNA encoding tyrosinase from Japanese quail and snapping turtle. These nonmammalian cDNA are highly homologous to those of the mouse and human tyrosinases, whereas the 5' flanking sequences are far less conserved except for a few short sequence motifs. Nevertheless, we demonstrate that the 5' flanking sequences from the quail or turtle tyrosinase genes are capable of directing the expression of a fused mouse tyrosinase cDNA when introduced into cultured mouse albino melanocytes. This experimental method, which reveals the functional conservation of regulatory sequences in one cell type (the melanocyte), may be utilized to evaluate phylogenetic differences in mechanisms controlling specific gene expression in many other types of cells. We also provide evidence that the 5' flanking sequences from these nonmammalian genes are functional in vivo by producing transgenic mice. Phylogenetic changes of vertebrate tyrosinase promoters and the possible involvement of conserved sequence motifs in melanocyte-specific expression of tyrosinase are discussed. PMID:11764277

Sato, S; Tanaka, M; Miura, H; Ikeo, K; Gojobori, T; Takeuchi, T; Yamamoto, H

2001-11-01

48

Effects of contour hedgerows on water and soil conservation, crop productivity and nutrient budget for slope farmland in the Three Gorges Region (TGR) of China  

Microsoft Academic Search

Soil erosion has long been recognized as a major environmental problem in the Three Gorges Region (TGR) where slope farming\\u000a is commonly practiced but the local topography is hilly. In consideration of the poor socioeconomic position of local farmers,\\u000a low cost hedgerows had been introduced as a soil conservation measure to the TGR in the late 1980s. A collaborative research

Sai Leung Ng; Qiang Guo Cai; Shu Wan Ding; Kwai Cheong Chau; Jie Qin

2008-01-01

49

PUBLIC CONSERVATION LAND AND EMPLOYMENT GROWTH IN THE NORTHERN FOREST REGION  

Microsoft Academic Search

As with many environmental issues, debates about increasing public conservation lands in the Northern Forest region frequently center on a perceived tradeoff between jobs and the environment. In particular, opponents of conservation lands often argue that employment will decline significantly when land is diverted from commodity-oriented uses such as wood products production. To evaluate this claim, we estimate a model

David A. Lewis; Gary L. Hunt; Andrew J. Plantinga

2001-01-01

50

Title: Public Conservation Land and Employment Growth in the Northern Forest Region  

Microsoft Academic Search

Abstract: As with many environmental issues, debates about increasing public conservation lands in the Northern Forest region frequently center on a perceived tradeoff between jobs and the environment. In particular, opponents of conservation lands often argue that employment,will decline significantly when land is diverted from commodity- oriented uses such as wood products production. To evaluate this claim, we estimate a

51

The conservation value of suburban golf courses in a rapidly urbanising region of Australia  

Microsoft Academic Search

The conservation value of suburban golf courses was assessed in southeast Queensland, Australia, by investigating their capacity to support urban-threatened birds, mammals, reptiles and frogs. Terrestrial vertebrate assemblages were compared between golf courses and nearby eucalypt fragments and with suburban bird assemblages. Biotic diversity varied among golf courses. While some had conservation value (supporting high densities of regionally threatened vertebrates),

S. C. Hodgkison; J.-M. Hero; J. Warnken

2007-01-01

52

Conserving migrating shorebirds in the Yellow Sea region  

Microsoft Academic Search

The Yellow Sea Region lies between North and South Korea to the east and China to the west, and covers an area of 458 000 sq km. Biodiversity in the inter-tidal zone of the Yellow Sea Region is high: excellent feeding and roosting areas accom- modate many different species of waterbirds, and preliminary records indicate that the coastal zone of

C. Kelin; X. Qiang

53

Conservation Strategy for Allotropa Virgata (Candystick), U. S. Forest Service, Northern and Intermountain Regions.  

National Technical Information Service (NTIS)

This conservation strategy provides recommendations for management of National Forest landssupporting and adjoining populations of Allotropa virgata (candystick), a plant speciesdesignated as sensitive in Regions 1 and 4 of the US Forest Service. Allotrop...

J. Lichthardt

1995-01-01

54

The status of chondrichthyan conservation in the Indo-Australasian region.  

PubMed

The status of chondrichthyan (sharks, batoids and chimaeras) conservation in the Indo-Australasian region is examined, and issues relevant to the conservation of this fauna at the subregional level [Australia, Indonesia (excluding West Papua), New Guinea (West Papua and Papua New Guinea), New Caledonia and New Zealand] are discussed. According to the 2009 IUCN Red List of Threatened Species, c. 21% of Indo-Australasian chondrichthyans are classified as threatened (critically endangered, endangered and vulnerable) and c. 40% are of conservation concern (threatened and near threatened). The proportion of threatened species is highest in New Guinea (c. 39%) and Indonesia (c. 35%) and least in New Zealand (c. 11%). In New Guinea, three quarters of the species are of conservation concern; in Indonesia, nearly two thirds are of conservation concern. Within the region, the proportion of threatened batoids (c. 29%) is higher than threatened sharks (c. 17%), while there are no threatened chimaeras. Conservation status is discussed at the order (for sharks), suborder (for batoids) and family level. Issues relating to the conservation status of chondrichthyans vary greatly between each subregion, but they mostly relate to targeted or incidental capture in fisheries. A handful of sharks and batoids are protected within Australian waters, while one species is protected in New Zealand. Both Australia and New Zealand have developed National Plans of Action for the Conservation and Management of Sharks (NPOA-Sharks), but these are lacking elsewhere. Development and implementation of NPOA-Sharks are a priority in order to drive the conservation of the regional fauna. Sustainable fisheries management (including by-catch), confronting the challenge of illegal, unreported and unregulated fishing, species protection where appropriate and marine protected areas (MPA) are all likely to prove vital in ensuring the long-term conservation of Indo-Australasian sharks, batoids and chimaeras. PMID:20557656

White, W T; Kyne, P M

2010-06-01

55

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

56

Monoclonal Antibodies Recognizing the Non-Tandem Repeat Regions of the Human Mucin MUC4 in Pancreatic Cancer  

PubMed Central

The MUC4 mucin is a high molecular weight, membrane-bound, and highly glycosylated protein. It is a multi-domain protein that is putatively cleaved into a large mucin-like subunit (MUC4?) and a C-terminal growth-factor like subunit (MUC4?). MUC4 plays critical roles in physiological and pathological conditions and is aberrantly overexpressed in several cancers, including those of the pancreas, cervix, breast and lung. It is also a potential biomarker for the diagnosis, prognosis and progression of several malignancies. Further, MUC4 plays diverse functional roles in cancer initiation and progression as evident from its involvement in oncogenic transformation, proliferation, inhibition of apoptosis, motility and invasion, and resistance to chemotherapy in human cancer cells. We have previously generated a monoclonal antibody 8G7, which is directed against the TR region of MUC4, and has been extensively used to study the expression of MUC4 in several malignancies. Here, we describe the generation of anti-MUC4 antibodies directed against the non-TR regions of MUC4. Recombinant glutathione-S-transferase (GST)-fused MUC4? fragments, both upstream (MUC4?-N-Ter) and downstream (MUC4?-C-Ter) of the TR domain, were used as immunogens to immunize BALB/c mice. Following cell fusion, hybridomas were screened using the aforementioned recombinant proteins ad lysates from human pancreatic cell lines. Three anti MUC4?-N-Ter and one anti-MUC4?-C-Ter antibodies were characterized by several inmmunoassays including enzyme-linked immunosorbent assay (ELISA), immunoblotting, immunofluorescene, flow cytometry and immunoprecipitation using MUC4 expressing human pancreatic cancer cell lines. The antibodies also reacted with the MUC4 in human pancreatic tumor sections in immunohistochemical analysis. The new domain-specific anti-MUC4 antibodies will serve as important reagents to study the structure-function relationship of MUC4 domains and for the development of MUC4-based diagnostics and therapeutics.

Jain, Maneesh; Venkatraman, Ganesh; Moniaux, Nicolas; Kaur, Sukhwinder; Kumar, Sushil; Chakraborty, Subhankar; Varshney, Grish C.; Batra, Surinder K.

2011-01-01

57

Distinct regions of influenza virus PB1 polymerase subunit recognize vRNA and cRNA templates.  

PubMed

The influenza virus RNA polymerase is a heterotrimer comprising the PB1, PB2 and PA subunits. PB1 is the core of the complex and accounts for the polymerase activity. We have studied the interaction of PB1 with model cRNA template by in vitro binding and Northwestern analyses. The binding to model cRNA was specific and showed an apparent Kd of approximately 7x10(-8) M. In contrast to the interaction with vRNA, PB1 was able to bind equally the 5' and 3' arm of the cRNA panhandle. The N-terminal 139 amino acids of PB1 and sequences between positions 267 and 493 proved positive for binding to cRNA, whereas the interaction with vRNA template previously was mapped to the N- and C-terminal regions. Competition experiments using the 5' and 3' arms of either the vRNA or cRNA panhandle indicated that the N-terminal binding site is shared by both templates. The data indicate that the PB1 RNA-binding sites are constituted by: (i) residues located at the N-terminus (probably common for vRNA and cRNA binding) and, either (ii) residues from the central part of PB1 (for cRNA) or (iii) residues from the C-terminal region of PB1 (for vRNA), and suggest that PB1 undergoes a conformational change upon binding to cRNA versus vRNA templates. PMID:10393191

González, S; Ortín, J

1999-07-01

58

Road, forestry and regional planners' work for biodiversity conservation and public participation: a case study in Poland's hotspot regions  

Microsoft Academic Search

We studied how regional, road and forestry planning sectors work to implement policies about biodiversity conservation and public participation. Evaluations were based on a normative model for planning derived from the existing international policies and relevant literature. Key planning actors were then interviewed with regard to their understanding of biodiversity and participation policies as well as ability to act and

Malgorzata Blicharska; Per Angelstam; Hans Antonson; Marine Elbakidze; Robert Axelsson

2011-01-01

59

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

60

Porcine B-cells recognize epitopes that are conserved between the structural proteins of American and European-type porcine reproductive and respiratory syndrome virus  

Microsoft Academic Search

By selecting phage display libraries with immune sera from experimentally infected pigs, porcine B-cell epitopes in the open reading frame (ORF) 2, 3, 5 and 6 proteins of European-type porcine reproductive and respiratory syndrome virus (PRRSV) were identified. The sequences of all the epitopes were well conserved in European-type PRRSV and even between European- and American-type PRRSV. Accordingly, sera from

M. B. Oleksiewicz; A. Břtner; P. Normann

2002-01-01

61

Landscape conservation genetics of Dipteryx alata ("baru" tree: Fabaceae) from Cerrado region of central Brazil.  

PubMed

In this paper random amplified polymorphic DNA (RAPD) was used to evaluate the degree of among-population differentiation and associated spatial patterns of genetic divergence for Dipteryx alata Vogel populations from Cerrado region of central Brazil, furnishing support for future programs of conservation of this species. We analyzed patterns of genetic and spatial population structure using 45 RAPD loci scored for 309 trees, sampled from five different regions with two populations each. Genetic structure analysis suggested that panmixia null hypothesis can be rejected, with significant among-population components of 15%. Hierarchical partition by Analysis of Molecular Variance (AMOVA) shows that 5% of genetic variation is within regions, whereas 10% of variation is among regions, and these results were confirmed by a Bayesian analyses on HICKORY. The Mantel correlogram revealed that this divergence is spatially structured, so that local populations situated at short geographic distances could not be considered independent units for conservation and management. However, genetic discontinuities among populations were found in the northwest and southeast parts of the study area, corresponding to regions of recent socio-economic expansion and high population density, respectively. Taking both geographic distances and genetic discontinuities into account it is possible to establish a group of population to be conserved, covering most of D. alata geographic distribution and congruent with previously established priority areas for conservation in the Cerrado region. PMID:17333479

Soares, Thannya Nascimento; Chaves, Lázaro José; de Campos Telles, Mariana Pires; Diniz-Filho, José Alexandre Felizola; Resende, Lucileide Vilela

2007-02-27

62

Human monoclonal antibody that recognizes the V3 region of human immunodeficiency virus gp120 and neutralizes the human T-lymphotropic virus type IIIMN strain.  

PubMed Central

We describe a human IgG1 monoclonal antibody (N701.9b) derived by Epstein-Barr virus transformation of B cells from a human immunodeficiency virus-seropositive asymptomatic donor. This antibody was shown to recognize the principal neutralizing domain contained within the V3 region of gp120 of the MN strain of human immunodeficiency virus and MN-like strains, as determined by binding to the PB-1 fragment of MN gp120 and to synthetic peptides corresponding to the V3 region of MN and related virus strains. The epitope identified by monoclonal antibody N701.9b was mapped to a segment of V3 containing at least 7 amino acids (amino acids 316-322), which is located in the "tip" and "right" side of the V3 loop of the MN strain. Furthermore, this antibody manifested potent type-specific fusion-inhibitory activity against the MN strain but not against the IIIB or RF virus strains. This antibody also neutralized four virus isolates that had MN-like V3 region sequences and failed to neutralize three other strains containing unrelated V3 region sequences. Our findings confirm that the V3 region stimulates type-specific neutralizing antibody during natural human immunodeficiency virus infection in humans. The potential clinical use of this antibody is discussed.

Scott, C F; Silver, S; Profy, A T; Putney, S D; Langlois, A; Weinhold, K; Robinson, J E

1990-01-01

63

Beta-globin locus activation regions: conservation of organization, structure, and function.  

PubMed

The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function. PMID:2236034

Li, Q L; Zhou, B; Powers, P; Enver, T; Stamatoyannopoulos, G

1990-11-01

64

Identification of receptor-interacting regions of vitellogenin within evolutionarily conserved ?-sheet structures by using a peptide array.  

PubMed

Vitellogenesis, a key process in oviparous animals, is characterized by enhanced synthesis of the lipoprotein vitellogenin, which serves as the major yolk-protein precursor. In most oviparous animals, and specifically in crustaceans, vitellogenin is mainly synthesized in the hepatopancreas, secreted to the hemolymph, and taken up into the ovary by receptor-mediated endocytosis. In the present study, localization of the vitellogenin receptor and its interaction with vitellogenin were investigated in the freshwater prawn Macrobrachium rosenbergii. The receptor was immuno-histochemically localized to the cell periphery and around yolk vesicles. A receptor blot assay revealed that the vitellogenin receptor interacts with most known vitellogenin subunits, the most prominent being the 79 kDa subunit. The receptor was, moreover, able to interact with trypsin-digested vitellogenin peptides. By combining a novel peptide-array approach with tandem mass spectrometry, eleven vitellogenin-derived peptides that interacted with the receptor were identified. A 3D model of vitellogenin indicated that four of the identified peptides are N-terminally localized. One of the peptides is homologous to the receptor-recognized site of vertebrate vitellogenin, and assumes a conserved ?-sheet structure. These findings suggest that this specific ?-sheet region in the vitellogenin N-terminal lipoprotein domain is the receptor-interacting site, with the rest of the protein serving to enhance affinity for the receptor. The conservation of the receptor recognition site in invertebrate and vertebrate vitellogenin might have vast implications for oviparous species reproduction, development, immunity, and pest management. PMID:23733483

Roth, Ziv; Weil, Simy; Aflalo, Eliahu D; Manor, Rivka; Sagi, Amir; Khalaila, Isam

2013-06-03

65

Conservation of crop diversity for sustainable landscape development in the mountains of the Indian Himalayan region  

Microsoft Academic Search

Purpose – The purpose of this paper is to emphasize the conservation and management of crop diversity in traditional agro-ecosystems as a crucial component for sustainable landscape development in the mountains of the Indian Himalayan region. The results indicate that mountain farming has the potential to produce good output from a low input system where farmers still use local resources

Sunil Nautiyal; Harald Kaechele

2007-01-01

66

The Significant Conservative and Variable Regions of the Homologous Protein Sequences  

Microsoft Academic Search

A method of identification of significant conservative and variable regions in homologous protein sequences is presented. A set of aligned homologous sequences is divided into two groups consisting of m and n most related sequences. Each pair of sequences from different group is compared using unitary similarity matrix. The superposition of pairwise comparisons scanned by a window of 10 amino

Pavel V. Kostetsky; Rimma R. Vladimirova

1992-01-01

67

Rational sub-division of plant trypanosomes ( Phytomonas spp.) based on minicircle conserved region analysis  

Microsoft Academic Search

The sequences of minicircle conserved regions from various plant trypanosomatids have been determined and analyzed. The goal of this study was to add another tool to the arsenal of molecular probes for distinguishing between the different trypanosomatids occuring in plants: systemic trypanosomatids multiplying in the sap, those from the laticiferous tubes, and those developing in fruits, seeds or flowers but

Nancy R. Sturm; Michel Dollet; Julius Lukesb; David A. Campbell

2007-01-01

68

Evolution and structural conservation of the control region of insect mitochondrial DNA  

Microsoft Academic Search

The control regions of mitochondrial DNA of two insects, Schistocerca gregaria and Chorthippus parallelus, have been isolated and sequenced. Their sizes are 752 by and 1,512 bp, respectively, with the presence of a tandem repeat in C. parallelus. (The sequences of the two repeats are highly conserved, having a homology of 97.5%.) Comparison of their nucleotide sequences revealed the presence

De-Xing Zhang; Jacek M. Szymura; Godfrey M. Hewitt

1995-01-01

69

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

70

Lift and Drag Prediction in Supersonic Region Based on Momentum Conservation Theory  

Microsoft Academic Search

Recently, as advanced drag prediction method in transonic region, a drag decomposition method is watched with keen interest. This method is based on and extended from the momentum conservation theory on the closed integral surface around the airplane, which is usually called `Control Volume Method' (CVM). In this paper, aiming the next target which is the drag decomposition in supersonic

Wataru Yamazaki; Kazuhiro Kusunose; Kisa Matsushima; Kazuhiro Nakahashi

2006-01-01

71

A highly conserved endonuclease activity present in Escherichia coli, bovine, and human cells recognizes oxidative DNA damage at sites of pyrimidines.  

PubMed Central

We have compared the sites of nucleotide incision on DNA damaged by oxidizing agents when cleavage is mediated by either Escherichia coli endonuclease III or an endonuclease present in bovine and human cells. E. coli endonuclease III, the bovine endonuclease isolated from calf thymus, and the human endonuclease partially purified from HeLa and CEM-C1 lymphoblastoid cells incised DNA damaged with osmium tetroxide, ionizing radiation, or high doses of UV light at sites of pyrimidines. For each damaging agent studied, regardless of whether the E. coli, bovine, or human endonuclease was used, the same sequence specificity of cleavage was observed. We detected this endonuclease activity in a variety of human fibroblasts derived from normal individuals as well as individuals with the DNA repair deficiency diseases ataxia telangiectasia and xeroderma pigmentosum. The highly conserved nature of such a DNA damage-specific endonuclease suggests that a common pathway exists in bacteria, humans, and other mammals for the reversal of certain types of oxidative DNA damage. Images

Doetsch, P W; Henner, W D; Cunningham, R P; Toney, J H; Helland, D E

1987-01-01

72

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

73

Assessing and Prioritizing Ecological Communities for Monitoring in a Regional Habitat Conservation Plan  

NASA Astrophysics Data System (ADS)

In nature reserves and habitat conservation areas, monitoring is required to determine if reserves are meeting their goals for preserving species, ecological communities, and ecosystems. Increasingly, reserves are established to protect multiple species and communities, each with their own conservation goals and objectives. As resources are always inadequate to monitor all components, criteria must be applied to prioritize both species and communities for monitoring and management. While methods for prioritizing species based on endangerment or risk have been established, approaches to prioritizing ecological communities for monitoring are not well developed, despite a long-standing emphasis on communities as target elements in reserve design. We established guidelines based on four criteria derived from basic principles of conservation and landscape ecology—extent, representativeness, fragmentation, and endangerment—to prioritize communities in the San Diego Multiple Species Conservation Plan (MSCP). The MSCP was one of the first multiple-species habitat conservation areas established in California, USA, and it has a complex spatial configuration because of the patterns of surrounding land use, which are largely urbanized. In this case study, high priority communities for monitoring include coastal sage scrub (high endangerment, underrepresented within the reserve relative to the region, and moderately fragmented), freshwater wetlands, and coastal habitats (both have high fragmentation, moderate endangerment and representativeness, and low areal extent). This framework may be useful to other conservation planners and land managers for prioritizing the most significant and at-risk communities for monitoring.

Hierl, Lauren A.; Franklin, Janet; Deutschman, Douglas H.; Regan, Helen M.; Johnson, Brenda S.

2008-07-01

74

Complementary functions of E1a conserved region 1 cooperate with conserved region 3 to activate adenovirus serotype 5 early promoters.  

PubMed Central

The amino-terminal region of the adenovirus type 5 E1a protein including conserved regions (CRs) 1 and 2 binds the 105-kDa retinoblastoma protein and a second, 300-kDa, cellular protein. We show that mutant viruses with deletions of CR1 which release the binding of either p105 or p300 still activate early promoters and infect cells productively. However, mutations which disrupt binding of both proteins disrupt early promoter activity and block the viral life cycle. Ela CR3, which has an established role in early promoter activation, can act in trans to the amino-terminal functions. This suggests that the amino terminus provides distinct, redundant functions related to p300 and Rb binding that synergize with CR3 to transactivate early genes. Images

Wong, H K; Ziff, E B

1994-01-01

75

Immunogenic epitopes of Hantaviruses' N protein are restricted to conserved regions.  

PubMed

The Bunyaviridae virus family is composed by five genera, of which the Hantavirus genus is one of the most important representatives. Occasionally, these viruses can be transmitted to humans, giving rise to severe diseases that present high mortality rates. We analyzed the amino acid sequences of the nucleocapsid (N) proteins of 34 different hantaviruses to investigate the potential mechanisms involved in immunogenicity against hantaviruses. Immunogenic epitopes described in the literature through experimental analyses for Sin Nombre (SNV), Puumala (PUUV), and Hantaan (HTNV) viruses' species were retrieved. We identified and characterized the regions believed to be responsible for the induction of immune response in hosts. We found that N protein epitopes described in the literature for PUUV, SNV and HTNV viruses are all located in highly conserved regions of the protein. The high conservation of these regions suggests that a cross-reactive immune response among different hantaviruses can be induced. PMID:22201821

Rigo, Mauricio Menegatti; Antunes, Dinler Amaral; Cibulski, Samuel Paulo; Sinigaglia, Marialva; Chies, Jose Artur Bogo; Vieira, Gustavo Fioravanti

2012-01-01

76

Novel bacterial lipoprotein structures conserved in low-GC content gram-positive bacteria are recognized by Toll-like receptor 2.  

PubMed

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. PMID:22303020

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

2012-02-02

77

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

78

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

79

Ecosystem service benefits of contrasting conservation strategies in a human-dominated region  

PubMed Central

The hope among policy-makers and scientists alike is that conservation strategies designed to protect biodiversity also provide direct benefits to people by protecting other vital ecosystem services. The few studies that have examined the delivery of ecosystem services by existing conservation efforts have concentrated on large, ‘wilderness’-style biodiversity reserves. However, such reserves are not realistic options for densely populated regions. Here, we provide the first analyses that compare representation of biodiversity and three other ecosystem services across several contrasting conservation strategies in a human-dominated landscape (England). We show that small protected areas and protected landscapes (restrictive zoning) deliver high carbon storage and biodiversity, while existing incentive payment (agri-environment) schemes target areas that offer little advantage over other parts of England in terms of biodiversity, carbon storage and agricultural production. A fourth ecosystem service—recreation—is under-represented by all three strategies. Our findings are encouraging as they illustrate that restrictive zoning can play a major role in protecting natural capital assets in densely populated regions. However, trade-offs exist even among the four ecosystem services we considered, suggesting that a portfolio of conservation and sustainability investments will be needed to deliver both biodiversity and the other ecosystem services demanded by society.

Eigenbrod, Felix; Anderson, Barbara J.; Armsworth, Paul R.; Heinemeyer, Andreas; Jackson, Sarah F.; Parnell, Mark; Thomas, Chris D.; Gaston, Kevin J.

2009-01-01

80

Functional Analyses of a Conserved Region in Glucosyltransferases of Streptococcus mutans  

Microsoft Academic Search

Streptococcus mutans glucosyltransferases (GTFs; GtfB, -C, and -D) synthesize water-soluble and -insoluble glucan polymers from sucrose. We have identified previously a conserved region of 19 amino acids (aa) (Gtf-P1; aa 409 to 427 of GtfB and aa 435 to 453 of GtfC) which is functionally important for both enzymatic activity and bacterial adherence. Monoclonal antibodies directed against Gtf-P1 selectively inhibited

JEAN-SAN CHIA; CZAU-SIUNG YANG; JEN-YANG CHEN

1998-01-01

81

Two B cell factors bind the HLA-DRA X box region and recognize different subsets of HLA class II promoters.  

PubMed

The class II genes of the human Major Histocompatibility Complex (MHC) encode three isotypes of alpha/beta heterodimeric proteins, HLA-DR, -DQ, and -DP, which are responsible for presenting processed antigens to T helper lymphocytes. These MHC class II genes are expressed in a coordinate manner. The promoter regions of all MHC class II genes share a set of highly conserved elements that mediate different levels of tissue-specific and inducible transcription. One element, the X box, appears to be the major positive element in B cell-specific expression, and nuclear protein binding studies have subdivided this region into the X1 and X2 boxes. Regulatory Factor X (RFX) binds to the X1 box whereas several other factors have been described that bind to the X2 box. In this report, we further characterize the X1 binding protein RFX and show that RFX binds poorly to beta chain gene promoters. In particular, RFX does not bind to the DRB gene, which is expressed at the highest levels of all beta chain genes. In addition, we have identified an X2 box binding activity in human B cell extracts that binds with high affinity to the HLA-DRA promoter. This X2 binding protein, X2BP, binds to a different subset of class II promoters than does RFX. These findings suggest that coordinate regulation of class II expression may involve different combinations or arrangements of transcriptional elements and factors instead of a common set. PMID:1956787

Hasegawa, S L; Boss, J M

1991-11-25

82

Two B cell factors bind the HLA-DRA X box region and recognize different subsets of HLA class II promoters.  

PubMed Central

The class II genes of the human Major Histocompatibility Complex (MHC) encode three isotypes of alpha/beta heterodimeric proteins, HLA-DR, -DQ, and -DP, which are responsible for presenting processed antigens to T helper lymphocytes. These MHC class II genes are expressed in a coordinate manner. The promoter regions of all MHC class II genes share a set of highly conserved elements that mediate different levels of tissue-specific and inducible transcription. One element, the X box, appears to be the major positive element in B cell-specific expression, and nuclear protein binding studies have subdivided this region into the X1 and X2 boxes. Regulatory Factor X (RFX) binds to the X1 box whereas several other factors have been described that bind to the X2 box. In this report, we further characterize the X1 binding protein RFX and show that RFX binds poorly to beta chain gene promoters. In particular, RFX does not bind to the DRB gene, which is expressed at the highest levels of all beta chain genes. In addition, we have identified an X2 box binding activity in human B cell extracts that binds with high affinity to the HLA-DRA promoter. This X2 binding protein, X2BP, binds to a different subset of class II promoters than does RFX. These findings suggest that coordinate regulation of class II expression may involve different combinations or arrangements of transcriptional elements and factors instead of a common set. Images

Hasegawa, S L; Boss, J M

1991-01-01

83

Conservative evolution of the Mbc-DP region in anthropoid primates.  

PubMed

To determine the organization of the DP region in the Mbc of anthropoid primates, we constructed contig maps from cosmid clones of the chimpanzee and orangutan, representatives of the infraorder Catarrhini, as well as of the cotton-top tamarin, a representative of the infraorder Platyrrhini. We found the maps to be remarkably similar to each other and to the previously published map of the human DP region. In each of the four species, the DP region consists of four loci arranged in the same order (DPB2 . . . DPA2 . . . DPB1 . . . DPA1) and in the same transcriptional orientation (tail-to-tail). The regions in the four species are of approximately the same length and many of the restriction sites are shared between species. The inserts of most Alu elements, of a ribosomal protein pseudogene, and of an IgC epsilon-like pseudogene are found in corresponding positions in all four species. The data indicate that the human-type organization of the DP region was established before the divergence of the Catarrhini and Platyrrhini lines more than 37 million years ago and that it has remained principally intact since that time. This conservation of the DP region is in striking contrast to the evolutionary instability of certain other Mbc regions, in particular those occupied by the DRB or C4 and CYP21 loci. We interpret the stability of the DP region as an indication that the region is being phased out functionally. PMID:7901184

Grahovac, B; Schönbach, C; Brändle, U; Mayer, W E; Golubic, M; Figueroa, F; Trowsdale, J; Klein, J

1993-06-01

84

Conserved regions of the timeless (tim) clock gene in Drosophila analyzed through phylogenetic and functional studies.  

PubMed Central

Circadian (approximately 24-hr) rhythms in Drosophila melanogaster depend upon cyclic expression of the period (per) and timeless (tim) genes, which encode interacting components of the endogenous clock. The per gene has been isolated from other insects and, more recently, a per ortholog was found in mammals where its expression oscillates in a circadian fashion. We report here the complete sequence of a tim gene from another species, Drosophila virilis. TIM is better conserved than the PER protein is between these two species (76 vs. 54% overall amino acid identity), and putative functional domains, such as the PER interaction domains and the nuclear localization signal, are highly conserved. The acidic domain and the cytoplasmic localization domain, however, are within the least conserved regions. In addition, the initiating methionine in the D. virilis gene lies downstream of the proposed translation start for the original D. melanogaster tim cDNA and corresponds to the one used by D. simulans and D. yakuba. Among the most conserved parts of TIM is a region of unknown function near the N terminus. We show here that deletion of a 32 amino acid segment within this region affects rescue of rhythms in arrhythmic tim01 flies. Flies carrying a full-length tim transgene displayed rhythms with approximately 24-hr periods, indicating that a fully functional clock can be restored in tim01 flies through expression of a tim transgene. Deletion of the segment mentioned above resulted in very long activity rhythms with periods ranging from 30.5 to 48 hr.

Ousley, A; Zafarullah, K; Chen, Y; Emerson, M; Hickman, L; Sehgal, A

1998-01-01

85

Analysis of T cell receptor beta chains in Lewis rats with experimental allergic encephalomyelitis: conserved complementarity determining region 3  

PubMed Central

This study explores the usage of T cell antigen receptor (TCR) beta chain elements in Lewis rats with experimentally induced allergic encephalomyelitis (EAE). TCRs from 15 different T cell clones and hybridomas derived from animals immunized with myelin basic protein (MBP), and all having specificity for the 21-mer encephalitogenic fragment MBP 68-88, utilized V beta 8.2. In addition, there was a marked conservation of the first two amino acid residues of the junctional complementarity determining region 3 (CDR3) associated with the V beta 8.2 receptors. 12 of 15 contained an aspartic acid followed by serine regardless of the associated J beta element. At the nucleotide level, this conservation of AspSer residues was accomplished with few or no nongermline-encoded nucleotide (N) additions. A similar pattern of AspSer usage and N region nucleotide additions was observed in a number of V beta 8.2 isolates derived from MBP-immunized lymph nodes. In contrast, V beta 8.2 polymerase chain reaction amplified isolates from Lewis T cells activated with concanavalin A or from lymph nodes of complete Freund's adjuvant-immunized animals showed no AspSer utilization (0/31) in the CDR3, and four to nine N region nucleotide additions. We conclude from this finding that AspSer residues in the CDR3, limited N region nucleotide additions, along with V beta 8.2 sequences, contribute to TCR specificity for MBP 68-88. This raises the possibility that encephalitogenic, disease-causing T cells either represent a population that derives from late fetal life or alternatively, that they are rare cells with this particular TCR phenotype contributed to the T cell pool throughout adulthood and are selected by antigen. In either case, the CDR3 AspSer sequences as well as V beta 8.2 sequences are candidates for the receptor target structures recognized by regulator T cells in recovery from and resistance to active EAE. In this respect, a preliminary analysis of TCR utilization in three T cell clones specific for MBP 68-88 isolated from animals recovered from active EAE indicates that while all three use V beta 8.2, only one contains AspSer in the CDR3.

1991-01-01

86

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

87

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

88

Conserved 3?-Untranslated Region Sequences Direct Subcellular Localization of Chaperone Protein mRNAs in Neurons*  

PubMed Central

mRNA localization provides polarized cells with a locally renewable source of proteins. In neurons, mRNA translation can occur at millimeters to centimeters from the cell body, giving the dendritic and axonal processes a means to autonomously respond to their environment. Despite that hundreds of mRNAs have been detected in neuronal processes, there are no reliable means to predict mRNA localization elements. Here, we have asked what RNA elements are needed for localization of transcripts encoding endoplasmic reticulum chaperone proteins in neurons. The 3?-untranslated regions (UTRs) of calreticulin and Grp78/BiP mRNAs show no homology to one another, but each shows extensive regions of high sequence identity to their 3?UTRs in mammalian orthologs. These conserved regions are sufficient for subcellular localization of reporter mRNAs in neurons. The 3?UTR of calreticulin has two conserved regions, and either of these is sufficient for axonal and dendritic targeting. However, only nucleotides 1315–1412 show ligand responsiveness to neurotrophin 3 (NT3) and myelin-associated glycoprotein (MAG). This NT3- and MAG-dependent axonal mRNA transport requires activation of JNK, both for calreticulin mRNA and for other mRNAs whose axonal levels are commonly regulated by NT3 and MAG.

Vuppalanchi, Deepika; Coleman, Jennifer; Yoo, Soonmoon; Merianda, Tanuja T.; Yadhati, Akshay G.; Hossain, Jobayer; Blesch, Armin; Willis, Dianna E.; Twiss, Jeffery L.

2010-01-01

89

Identification of serotype-specific T cell responses to highly conserved regions of the dengue viruses.  

PubMed

Determining previous infecting dengue virus (DENV) serotypes has been difficult due to highly cross-reactive immune responses from previous DENV infections. Determining the correlates of serotype-specific immune responses would be crucial in understanding dengue transmission in the community and would also help to determine the correlates of protective immune responses. Therefore, we set out to define highly conserved, serotype-specific regions of the DENVs. Serotype-specific and highly conserved regions of the four DENV serotypes were identified using Basic Local Alignment Search Tool (BLAST) searches and custom perl scripts. Using ex-vivo and cultured enzyme-linked immunospot (ELISPOT) assays, we identified serotype-specific T cell epitopes within the four DENV serotypes in healthy adult donors from Sri Lanka. We identified T cell responses to 19 regions of the four DENV serotypes. Six peptides were from the NS2A region and four peptides were from the NS4A region. All immune donors responded to peptides of at least two DENV serotypes, suggesting that heterologous infection is common in Sri Lanka. Eight of 20 individuals responded to at least two peptides of DENV-4, despite this serotype not being implicated previously in any of the epidemics in Sri Lanka. The use of these regions to determine past and current infecting DENV serotypes will be of value to characterize further the dynamics of silent dengue transmission in the community. In addition, these T cell responses to these regions could be used to characterize DENV serotype-specific immune responses and thus possibly help us to understand the immune correlates of a protective immune response. PMID:22471283

Malavige, G N; McGowan, S; Atukorale, V; Salimi, M; Peelawatta, M; Fernando, N; Jayaratne, S D; Ogg, G

2012-05-01

90

Identification of serotype-specific T cell responses to highly conserved regions of the dengue viruses  

PubMed Central

Determining previous infecting dengue virus (DENV) serotypes has been difficult due to highly cross-reactive immune responses from previous DENV infections. Determining the correlates of serotype-specific immune responses would be crucial in understanding dengue transmission in the community and would also help to determine the correlates of protective immune responses. Therefore, we set out to define highly conserved, serotype-specific regions of the DENVs. Serotype-specific and highly conserved regions of the four DENV serotypes were identified using Basic Local Alignment Search Tool (BLAST) searches and custom perl scripts. Using ex-vivo and cultured enzyme-linked immunospot (ELISPOT) assays, we identified serotype-specific T cell epitopes within the four DENV serotypes in healthy adult donors from Sri Lanka. We identified T cell responses to 19 regions of the four DENV serotypes. Six peptides were from the NS2A region and four peptides were from the NS4A region. All immune donors responded to peptides of at least two DENV serotypes, suggesting that heterologous infection is common in Sri Lanka. Eight of 20 individuals responded to at least two peptides of DENV-4, despite this serotype not being implicated previously in any of the epidemics in Sri Lanka. The use of these regions to determine past and current infecting DENV serotypes will be of value to characterize further the dynamics of silent dengue transmission in the community. In addition, these T cell responses to these regions could be used to characterize DENV serotype-specific immune responses and thus possibly help us to understand the immune correlates of a protective immune response.

Malavige, G N; McGowan, S; Atukorale, V; Salimi, M; Peelawatta, M; Fernando, N; Jayaratne, S D; Ogg, G

2012-01-01

91

Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate  

PubMed Central

Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.

Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2013-01-01

92

Lift and Drag Prediction in Supersonic Region Based on Momentum Conservation Theory  

NASA Astrophysics Data System (ADS)

Recently, as advanced drag prediction method in transonic region, a drag decomposition method is watched with keen interest. This method is based on and extended from the momentum conservation theory on the closed integral surface around the airplane, which is usually called ‘Control Volume Method’ (CVM). In this paper, aiming the next target which is the drag decomposition in supersonic flows, the validation study of the CVM in the supersonic region was conducted. Two dimensional structured mesh computation of NACA0012 airfoil was used for the investigation. At the lift and drag prediction using the CVM in the supersonic region, the discontinuous variation or oscillation of the lift and drag value was observed when the integral surface was set to some particular positions related to the generated shock waves. By the avoidance of the inappropriate positions, however, the good performance of the lift and drag prediction using CVM was achieved.

Yamazaki, Wataru; Kusunose, Kazuhiro; Matsushima, Kisa; Nakahashi, Kazuhiro

93

A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution  

PubMed Central

The molecular mechanism and physiological function of recoding by A-to-I RNA editing is well known, but its evolutionary significance remains a mystery. We analyzed the RNA editing of the Kv2 K+ channel from different insects spanning more than 300 million years of evolution: Drosophila melanogaster, Culex pipiens (Diptera), Pulex irritans (Siphonaptera), Bombyx mori (Lepidoptera), Tribolium castaneum (Coleoptera), Apis mellifera (Hymenoptera), Pediculus humanus (Phthiraptera), and Myzus persicae (Homoptera). RNA editing was detected across all Kv2 orthologs, representing the most highly conserved RNA editing event yet reported in invertebrates. Surprisingly, five of these editing sites were conserved in squid (Mollusca) and were possibly of independent origin, suggesting phylogenetic conservation of editing between mollusks and insects. Based on this result, we predicted and experimentally verified two novel A-to-I editing sites in squid synaptotagmin I transcript. In addition, comparative analysis indicated that RNA editing usually occurred within highly conserved coding regions, but mostly altered less-conserved coding positions of these regions. Moreover, more than half of these edited amino acids are genomically encoded in the orthologs of other species; an example of a conversion model of the nonconservative edited site is addressed. Therefore, these data imply that RNA editing might play dual roles in evolution by extending protein diversity and maintaining phylogenetic conservation.

Yang, Yun; Lv, Jianning; Gui, Bin; Yin, Heng; Wu, Xiaojie; Zhang, Yaozhou; Jin, Yongfeng

2008-01-01

94

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

95

The economics of biodiversity conservation: a study of a coffee growing region in the Western Ghats of India  

Microsoft Academic Search

This paper analyses the economics of biodiversity conservation in the context of a tropical forest ecosystem in the Western Ghats region of India, where coffee is the main competitor for land use. Using primary data covering a cross-section of coffee growers, the study notes that the opportunity costs of biodiversity conservation in terms of coffee benefits foregone are quite high.

K. N. Ninan; Jyothis Sathyapalan

2005-01-01

96

New Estimates of Massachusetts Old-growth Forests: Useful Data for Regional Conservation and Forest Reserve Planning  

Microsoft Academic Search

Old-growth forests are currently identified as core components of regional conservation and forest-reserve planning efforts by agencies and organizations across the northeastern United States. Despite the importance of these ecosystems from an ecological and conservation standpoint, major questions remain concerning their actual extent, location, and configuration in many states. Here we report a substantially revised estimate for individual tracts and

Anthony W. D'Amato; David A. Orwig; David R. Foster

2006-01-01

97

Water Use Conservation Scenarios for the Mississippi Delta Using an Existing Regional Groundwater Flow Model  

NASA Astrophysics Data System (ADS)

The alluvial plain in northwestern Mississippi, locally referred to as the Delta, is a major agricultural area, which contributes significantly to the economy of Mississippi. Land use in this area can be greater than 90 percent agriculture, primarily for growing catfish, corn, cotton, rice, and soybean. Irrigation is needed to smooth out the vagaries of climate and is necessary for the cultivation of rice and for the optimization of corn and soybean. The Mississippi River Valley alluvial (MRVA) aquifer, which underlies the Delta, is the sole source of water for irrigation, and over use of the aquifer has led to water-level declines, particularly in the central region. The Yazoo-Mississippi-Delta Joint Water Management District (YMD), which is responsible for water issues in the 17-county area that makes up the Delta, is directing resources to reduce the use of water through conservation efforts. The U.S. Geological Survey (USGS) recently completed a regional groundwater flow model of the entire Mississippi embayment, including the Mississippi Delta region, to further our understanding of water availability within the embayment system. This model is being used by the USGS to assist YMD in optimizing their conservation efforts by applying various water-use reduction scenarios, either uniformly throughout the Delta, or in focused areas where there have been large groundwater declines in the MRVA aquifer.

Barlow, J. R.; Clark, B. R.

2010-12-01

98

Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice.  

PubMed Central

Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leriathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.

Chen, M; SanMiguel, P; Bennetzen, J L

1998-01-01

99

Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences  

Microsoft Academic Search

The gene identification procedure in a completely new gene with no good homology with protein sequences can be a very complex task. In order to identify the protein-coding region, a new method, `SYNCOD', based on the analysis of conservative evolutionary properties of coding regions, has been realized. This program is able to identify and use the coding region homologies of

Igor B Rogozin; Dino D'Angelo; Luciano Milanesi

1999-01-01

100

The Association Between Biological Subtype and Isolated Regional Nodal Failure After Breast-Conserving Therapy  

SciTech Connect

Purpose: To evaluate the risk of isolated regional nodal failure (RNF) among women with invasive breast cancer treated with breast-conserving surgery (BCS) and radiation therapy (RT) and to determine factors, including biological subtype, associated with RNF. Methods and Materials: We retrospectively studied 1,000 consecutive women with invasive breast cancer who received breast-conserving surgery and RT from 1997 through 2002. Ninety percent of patients received adjuvant systemic therapy; none received trastuzumab. Sentinel lymph node biopsy was done in 617 patients (62%). Of patients with one to three positive nodes, 34% received regional nodal irradiation (RNI). Biological subtype classification into luminal A, luminal B, HER-2, and basal subtypes was based on estrogen receptor status-, progesterone receptor status-, and HER-2-status of the primary tumor. Results: Median follow-up was 77 months. Isolated RNF occurred in 6 patients (0.6%). On univariate analysis, biological subtype (p = 0.0002), lymph node involvement (p = 0.008), lymphovascular invasion (p = 0.02), and Grade 3 histology (p = 0.01) were associated with significantly higher RNF rates. Compared with luminal A, the HER-2 (p = 0.01) and basal (p = 0.08) subtypes were associated with higher RNF rates. The 5-year RNF rate among patients with one to three positive nodes treated with tangents alone was 2.4%; we could not identify a subset of these patients with a substantial risk of RNF. Conclusions: Isolated RNF is a rare occurrence after breast-conserving therapy. Patients with the HER-2 (not treated with trastuzumab) and basal subtypes appear to be at higher risk of developing RNF although this risk is not high enough to justify the addition of RNI. Low rates of RNF in patients with one to three positive nodes suggest that tangential RT without RNI is reasonable in most patients.

Wo, Jennifer Y. [Harvard Radiation Oncology Program, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Taghian, Alphonse G. [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Nguyen, Paul L. [Harvard Radiation Oncology Program, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Raad, Rita Abi [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Sreedhara, Meera B.A.; Bellon, Jennifer R.; Wong, Julia S. [Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Gadd, Michele A.; Smith, Barbara L. [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Harris, Jay R., E-mail: jharris@lroc.harvard.ed [Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States)

2010-05-01

101

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

102

Diversity and distribution of aquatic insects in Southern Brazil wetlands: implications for biodiversity conservation in a Neotropical region.  

PubMed

The selection of priority areas is an enormous challenge for biodiversity conservation. Some biogeographic methods have been used to identify the priority areas to conservation, and panbiogeography is one of them. This study aimed at the utilization of panbiogeographic tools, to identify the distribution patterns of aquatic insect genera, in wetland systems of an extensive area in the Neotropical region (approximately 280 000km2), and to compare the distribution of the biogeographic units identified by the aquatic insects, with the conservation units of Southern Brazil. We analyzed the distribution pattern of 82 genera distributed in four orders of aquatic insects (Diptera, Odonata, Ephemeroptera and Trichoptera) in Southern Brazil wetlands. Therefore, 32 biogeographic nodes corresponded to the priority areas for conservation of the aquatic insect diversity. Among this total, 13 were located in the Atlantic Rainforest, 16 in the Pampa and three amongst both biomes. The distribution of nodes showed that only 15% of the dispersion centers of insects were inserted in conservation units. The four priority areas pointed by node cluster criterion must be considered in further inclusions of areas for biodiversity conservation in Southern Brazil wetlands, since such areas present species from different ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region. PMID:22458224

Maltchik, Leonardo; Dalzochio, Marina Schmidt; Stenert, Cristina; Rolon, Ana Silvia

2012-03-01

103

Highly conserved regions of influenza a virus polymerase gene segments are critical for efficient viral RNA packaging.  

PubMed

The genome of the influenza A virus is composed of eight different segments of negative-sense RNA. These eight segments are incorporated into budding virions in an equimolar ratio through a mechanism that is not fully understood. Two different models have been proposed for packaging the viral ribonucleoproteins into newly assembling virus particles: the random-incorporation model and the selective-incorporation model. In the last few years, increasing evidence from many different laboratories that supports the selective-incorporation model has been accumulated. In particular, different groups have shown that some large viral RNA regions within the coding sequences at both the 5' and 3' ends of almost every segment are sufficient for packaging foreign RNA sequences. If the packaging regions are crucial for the viability of the virus, we would expect them to be conserved. Using large-scale analysis of influenza A virus sequences, we developed a method of identifying conserved RNA regions whose conservation cannot be explained by population structure or amino acid conservation. Interestingly, the conserved sequences are located within the regions identified as important for efficient packaging. By utilizing influenza virus reverse genetics, we have rescued mutant viruses containing synonymous mutations within these highly conserved regions. Packaging of viral RNAs in these viruses was analyzed by reverse transcription using a universal primer and quantitative PCR for individual segments. Employing this approach, we have identified regions in the polymerase gene segments that, if mutated, result in reductions of more than 90% in the packaging of that particular polymerase viral RNA. Reductions in the level of packaging of a polymerase viral RNA frequently resulted in reductions of other viral RNAs as well, and the results form a pattern of hierarchy of segment interactions. This work provides further evidence for a selective packaging mechanism for influenza A viruses, demonstrating that these highly conserved regions are important for efficient packaging. PMID:18094182

Marsh, Glenn A; Rabadán, Raúl; Levine, Arnold J; Palese, Peter

2007-12-19

104

Structural analysis of the 5? region of mouse and human huntington disease genes reveals conservation of putative promoter region and di- and trinucleotide polymorphisms  

Microsoft Academic Search

We have previously cloned and characterized the murine homologue of the Huntington disease (HD) gene and shown that it maps to mouse chromosome 5 within a region of conserved synteny with human chromosome 4p16.3. Here we present a detailed comparison of the sequence of the putative promoter and the organization of the 5? genomic region of the murine (Hdh) and

Biaoyang Lin; Jamal Nasir; Michael A. Kalchman; Helen Mcdonald; Jutta Zeisler; Y. Paul Goldberg; Michael R. Hayden

1995-01-01

105

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions  

PubMed Central

Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions.

Royo, Jose Luis; Hidalgo, Carmen; Roncero, Yolanda; Seda, Maria Angeles; Akalin, Altuna; Lenhard, Boris; Casares, Fernando; Gomez-Skarmeta, Jose Luis

2011-01-01

106

Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.  

PubMed

Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions. PMID:21935474

Royo, José Luis; Hidalgo, Carmen; Roncero, Yolanda; Seda, María Angeles; Akalin, Altuna; Lenhard, Boris; Casares, Fernando; Gómez-Skarmeta, José Luis

2011-09-13

107

The Prp19 WD40 Domain Contains a Conserved Protein Interaction Region Essential for its Function  

PubMed Central

Summary Prp19 is a member of the WD40-repeat family of E3 ubiquitin ligases and a conserved eukaryotic RNA splicing factor essential for activation and stabilization of the spliceosome. To understand the role of the WD40 repeat domain of Prp19 we have determined its structure using X-ray crystallography. The domain has a distorted seven bladed WD40 architecture with significant asymmetry due to irregular packing of blades one and seven into the core of the WD40 domain. Structure-based mutagenesis identified a highly conserved surface centered around blade five that is required for the physical interaction between Prp19 and Cwc2, another essential splicing factor. This region is found to be required for Prp19 function and yeast viability. Experiments in vitro and in vivo demonstrate that two molecules of Cwc2 bind to the Prp19 tetramer. These coupled structural and functional studies provide a model for the functional architecture of Prp19.

Vander Kooi, Craig W.; Ren, Liping; Xu, Ping; Ohi, Melanie D.; Gould, Kathleen L.; Chazin, Walter J.

2010-01-01

108

Ancient conserved regions in new gene sequences and the protein databases  

SciTech Connect

Sets of new gene sequences from human, nematode, and yeast were compared with each other and with a set of Escherichia coli genes in order to detect ancient evolutionarily conserved regions (ACRs) in the encoded proteins. Nearly all of the ACRs so identified were found to be homologous to sequences in the protein databases. This suggests that currently known proteins may already include representatives of most ACRs and that new sequences not similar to any database sequence are unlikely to contain ACRs. Preliminary analyses indicate that moderately expressed genes may be more likely to contain ACRs than rarely expressed genes. It is estimated that there are fewer than 900 ACRs in all. 20 refs., 2 figs., 4 tabs.

Green, P.; Hillier, L.; Waterston, R. (Washington Univ., St Louis, MO (United States)); Lipman, D.; States, D.; Claverie, J.M. (National Institutes of Health, Bethesda, MD (United States))

1993-03-19

109

Autoantibodies from patients with primary biliary cirrhosis recognize a restricted region within the cytoplasmic tail of nuclear pore membrane glycoprotein Gp210  

PubMed Central

Patients with primary biliary cirrhosis (PBC) frequently have autoantibodies against a 210-kD integral glycoprotein of the nuclear envelope pore membrane. This protein, termed gp210, has a 1,783-amino acid amino-terminal domain located in the perinuclear space, a 20-amino acid transmembrane segment, and a 58-amino acid cytoplasmic carboxy- terminal tail. We now demonstrate that autoantibodies from 25 patients with PBC that recognize gp210 react with the cytoplasmic carboxy- terminal tail while none react with unmodified linear epitopes in the amino-terminal domain. The epitope(s) recognized by autoantibodies from all 25 patients is contained within a stretch of 15 amino acids. The recognized amino acid sequence is homologous to the protein products of the Escherichia coli mutY gene and Salmonella typhimurium mutB gene with an exact identity of six consecutive amino acids, suggesting that anti-gp210 antibodies may arise by molecular mimicry of bacterial antigenic determinants.

1993-01-01

110

Identification of Conserved Regions and Residues within Hedgehog Acyltransferase Critical for Palmitoylation of Sonic Hedgehog  

PubMed Central

Background Sonic hedgehog (Shh) is a palmitoylated protein that plays key roles in mammalian development and human cancers. Palmitoylation of Shh is required for effective long and short range Shh-mediated signaling. Attachment of palmitate to Shh is catalyzed by Hedgehog acyltransferase (Hhat), a member of the membrane bound O-acyl transferase (MBOAT) family of multipass membrane proteins. The extremely hydrophobic composition of MBOAT proteins has limited their biochemical characterization. Except for mutagenesis of two conserved residues, there has been no structure-function analysis of Hhat, and the regions of the protein required for Shh palmitoylation are unknown. Methodology/Principal Findings Here we undertake a systematic approach to identify residues within Hhat that are required for protein stability and/or enzymatic activity. We also identify a second, novel MBOAT homology region (residues 196–234) that is required for Hhat activity. In total, ten deletion mutants and eleven point mutants were generated and analyzed. Truncations at the N- and C-termini of Hhat yielded inactive proteins with reduced stability. Four Hhat mutants with deletions within predicted loop regions and five point mutants retained stability but lost palmitoylation activity. We purified two point mutants, W378A and H379A, with defective Hhat activity. Kinetic analyses revealed alterations in apparent Km and Vmax for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants. Conclusions/Significance This study has pinpointed specific regions and multiple residues that regulate Hhat stability and catalysis. Our findings should be applicable to other MBOAT proteins that mediate lipid modification of Wnt proteins and ghrelin, and should serve as a model for understanding how secreted morphogens are modified by palmitoyl acyltransferases.

Buglino, John A.; Resh, Marilyn D.

2010-01-01

111

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

112

Transcribed-ultra conserved region expression profiling from low-input total RNA  

PubMed Central

Background Ultra Conserved Regions (UCRs) are a class of 481 noncoding sequences located in both intra- and inter-genic regions of the genome. The recent findings that they are significantly altered in adult chronic lymphocytic leukemias, carcinomas, and pediatric neuroblastomas lead to the hypothesis that UCRs may play a role in tumorigenesis. Results We present a novel application of Ribo-SPIA™ isothermal linear amplification of minute RNA quantities for quantifying Transcribed-UCR (T-UCR) expression by quantitative PCR. Direct comparison of non-amplified with amplified cDNA in two neuroblastoma cell lines showed that the amplification approach increases sensitivity and repeatability in T-UCR quantification. It is noteworthy that the Ribo-SPIA™ step allowed us to analyze all 481 T-UCRs by using 150 ng of RNA, while introducing a minimal bias and preserving the magnitude of relative expression. Only the less abundant T-UCRs have high intra-assay variability, consistently with the Poisson distribution statistics and stochastic effects on PCR repeatability. Conclusions We demonstrated that the quantification procedure shown here is an accurate and reliable technique for genome-wide non coding gene (i.e., UCRs) profiling using small amounts of RNA. This issue is particularly important because studies of transcription regulation are increasingly conducted in small homogeneous samples, such as laser capture microdissected or sorted cell populations.

2010-01-01

113

Conservation value of a native forest fragment in a region of extensive agriculture.  

PubMed

A survey of mammals and birds was carried out in a semi-deciduous forest fragment of 150 ha located in a zone of intensive agriculture in Ribeirăo Preto, State of Săo Paulo, south-eastern Brazil. Line transect sampling was used to census mammals and birds during six days, totalling 27.8 km of trails and 27.8 hours of observation. Twenty mammal species were confirmed in the area (except bats and small mammals), including rare or endangered species, such as the mountain lion (Puma concolor), the maned wolf (Chrysocyon brachyurus), and the ocelot (Leopardus pardalis). The brown capuchin monkey (Cebus apella) and the black-tufted-ear marmoset (Callithrix penicillata) were found frequently, suggesting high population density in the fragment. Regarding the avifauna, 49 bird species were recorded, most of them typical of open areas or forest edges. Some confirmed species, however, are becoming increasingly rare in the region, as for example the muscovy duck (Cairina moschata) and the toco toucan (Ramphastos toco). The results demonstrate that forest fragment of this size are refuges for native fauna in a region dominated almost exclusively by sugar-cane plantations. Besides faunal aspects, the conservation of these fragments is of great importance for the establishment of studies related to species preservation in the long term, including reintroduction and translocation projects, as well as studies related to genetic health of isolated populations. PMID:10959107

Chiarello

2000-05-01

114

From the Levant to Gibraltar: a regional perspective for marine conservation in the Mediterranean Sea.  

PubMed

Marine protected areas (MPAs) are critical to the well-being of threatened ecosystems and thus can be highly beneficial to humans, especially to those residing nearby. We explore the qualities of 117 MPAs in the Mediterranean basin and develop a taxonomy of their characteristics. We relate the spatial distribution of the MPAs to the various characteristics of the taxonomy (size, distance from shore, protection levels, management regimes, etc.) and to areas of high human impact and influence levels. To do this we use information on biogeographic regions and information from two different human influence models; one model developed for the marine environment and one covering the littoral terrestrial environment. Our analysis provides insights to planners and managers working in a regional capacity and trying to build MPA networks. Generally, current MPAs have not been established in high impact areas despite their being close to shores containing intense human activity. Decision-makers wishing to design and establish new MPAs may seek out areas of high cumulative human impacts (near the marine-terrestrial interface) or avoid them depending on marine conservation objectives, including the desire to vary types of MPAs within a network. Limitations of our analysis and methodology indicate areas for further research. PMID:22851348

Portman, Michelle E; Nathan, Daniel; Levin, Noam

2012-08-01

115

Duck nest success on Conservation Reserve Program land in the prairie pothole region  

USGS Publications Warehouse

Habitat fragmentation from intensified farming has concentrated nesting waterfowl and their predators in the remaining, relatively small untitled habitats of the prairie pothole region in the United States. The areas of land that have been enrolled in the Conservation Reserve Program (CRP) in this area could help disperse these concentrations and reduce losses to predators. The presence of CRP land may influence decisions about intensive management of public lands devoted to waterfowl production. During 1989-1991, waterfowl nest success on CRP fields in areas of high wetland density in the prairie pothole region was 23.1 percent compared to 8.2 percent on similar covers on federal waterfowl production areas. CRP fields thus provided more secure nesting cover for upland-nesting ducks than waterfowl production areas. However, nest success and use of the fields by ducks varied greatly. CRP fields are abundant and of a wide variety of age classes and sizes. These characteristics make CRP fields well suited as study sites for determining the effects of cover area, distance to water, and cover age on nest success of ducks.

Kantrud, H. A.

1993-01-01

116

[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

117

Mutations in the conserved woodchuck hepatitis virus polymerase FLLA and YMDD regions conferring resistance to lamivudine.  

PubMed

During more than 104 weeks of treatment with lamivudine (3TC) in chronic woodchuck hepatitis virus (WHV) carrier woodchucks, viral recrudescence occurred. Analysis of WHV DNA polymerase from woodchuck serum samples by PCR followed by DNA sequencing demonstrated that all samples were wild type at the conserved YMDD motif in domain C. Four of the six 3TC-treated woodchucks showed a mixture of the wild-type Ala (GCT) and the mutant Thr (ACT) at the conserved amino acid residue 566 (FLLA) in domain B of the WHV polymerase region. The appearance of the A566T mutation was temporally associated with viral recrudescence. This change is analogous with the amino acid 181 (FLLA) in HBV where 3TC selects for a change from Ala to Thr in humans. In the woodchuck, the Ala to Thr change in the polymerase gene results in a mutation of the WHV surface protein (amino acid 377) from Trp (TGG) to an opal codon (TGA), which may prematurely terminates the polypeptide. Three WHV molecular infectious clones were constructed to study this mutation in greater detail in vitro: A566T, analogous to A181T in HBV; M589V, analogous to the M204V in HBV; and the double mutant A566T/M589V, analogous to A181T/M204V in HBV. These mutants exhibited drug-sensitivity and replication profiles that paralleled those reported for analogous HBV variants. In transfected Huh7 cells, WHV containing the M589V mutation conferred at least 100-fold increased resistance to 3TC, but replicated approximately 5-fold less efficiently than wild-type virus as judged by both extracellular virus production and intracellular DNA replicative forms. In contrast, A566T mutant was approximately 10-fold more resistant to 3TC, replicated intracellularly as well as wild type, but produced 10-fold lower levels of virions than wild type. These findings are consistent with the observation that the A566T mutation alters the overlapping WHV surface antigen reading frame. WHV carrying mutations in the conserved YMDD motif, while not directly selected during lamivudine therapy in WHV carrier woodchucks, are replication competent in cell culture indicating the potential for their emergence in treated animals. These results further illustrate the utility of the WHV/woodchuck model to studies of HBV-drug resistance. PMID:12076758

Tatti, Kathleen M; Korba, Brent E; Stang, Heather L; Peek, Simon; Gerin, John L; Tennant, Bud C; Schinazi, Raymond F

2002-07-01

118

Analysis of peptidic epitopes recognized by the three monoclonal antibodies specific for the same region of glycophorin A but showing different properties.  

PubMed

Analysis of epitopes for the three monoclonal antibodies (GPA105, GPA33, OSK4-1) against glycophorin A (GPA) was performed with the use of proteolytic fragments of GPA, the synthetic nonapeptide with the sequence of amino acid residues 35-43 of GPA, and a series of peptides synthesized on plastic pins. The antibodies were specific for a short peptide sequence RAHE (a.a. 39-42 of GPA, MAbs GPA105 and OSK4-1) or RAHEV (a.a. 39-43 of GPA, MAb GPA33). Despite recognizing the same fragment of GPA, the three antibodies showed differences in fine specificity and in response to antigen desialylation. Reactions with single replacement analogs of the RAHEV sequence showed that immunodominant (unreplaceable) residues for the MAbs GPA33 and OSK4-1 were His and Glu, respectively, whereas no such residue was found for the MAb GPA105. Desialylation of the antigen gave strong enhancement of reactivity with the MAb GPA33, moderate--with the MAb GPA105, and weak or no enhancement of reaction with the MAb OSK4-1. The results showed that monoclonal antibodies directed against the same fragment of the polypeptide chain of densely glycosylated antigen may recognize different subsites which are masked at different degree by sialic acid residues. PMID:1376415

Wa?niowska, K; Duk, M; Czerwi?ski, M; Steuden, I; Du?, D; Radzikowski, C; Bartosz-Bechowski, H; Konopi?ska, D; Lisowska, E

1992-06-01

119

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

2013-09-12

120

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

121

Bovine papillomavirus-like particles presenting conserved epitopes from membrane-proximal external region of HIV-1 gp41 induced mucosal and systemic antibodies.  

PubMed

Two conserved epitopes, located in the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 (HIV-1) gp41, are recognized by two HIV-1 broadly neutralizing antibodies 2F5 and 4E10, and are promising targets for vaccine design in efforts to elicit anti-HIV-1 broadly neutralizing antibodies. Since most HIV-1 infections initiate at mucosal surfaces, induction of mucosal neutralizing antibodies is necessary and of utmost importance to counteract HIV-1 infection. Here, we utilized a mucosal vaccine vector, bovine papillomavirus (BPV) virus-like particles (VLPs), as a platform to present HIV-1 neutralizing epitopes by inserting the extended 2F5 or 4E10 epitope or the MPER domain into D-E loop of BPV L1 respectively. The chimeric VLPs presenting MPER domain resembled the HIV-1 natural epitopes better than the chimeric VLPs presenting single epitopes. Oral immunization of mice with the chimeric VLPs displaying the 2F5 epitope or MPER domain elicited epitope-specific serum IgGs and mucosal secretory IgAs. The induced antibodies specifically recognized the native conformation of MPER in the context of HIV-1 envelope protein. The antibodies induced by chimeric VLPs presenting MPER domain are able to partially neutralize HIV-1 viruses from clade B and clade C. PMID:24055348

Zhai, Yougang; Zhong, Zhenyu; Zariffard, Mohammadreza; Spear, Gregory T; Qiao, Liang

2013-09-19

122

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

PubMed

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. PMID:24089891

Yeo, U J; Supple, J R; Taylor, M L; Smith, R; Kron, T; Franich, R D

2013-10-01

123

Groucho binds two conserved regions of LEF-1 for HDAC-dependent repression  

PubMed Central

Background Drosophila Groucho and its human Transducin-like-Enhancer of Split orthologs (TLEs) function as transcription co-repressors within the context of Wnt signaling, a pathway with strong links to cancer. The current model for how Groucho/TLE's modify Wnt signaling is by direct competition with ?-catenin for LEF/TCF binding. The molecular events involved in this competitive interaction are not defined and the actions of Groucho/TLEs within the context of Wnt-linked cancer are unknown. Methods We used in vitro protein interaction assays with the LEF/TCF family member LEF-1, and in vivo assays with Wnt reporter plasmids to define Groucho/TLE interaction and repressor function. Results Mapping studies reveal that Groucho/TLE binds two regions in LEF-1. The primary site of recognition is a 20 amino acid region in the Context Dependent Regulatory domain. An auxiliary site is in the High Mobility Group DNA binding domain. Mutation of an eight amino acid sequence within the primary region (RFSHHMIP) results in a loss of Groucho action in a transient reporter assay. Drosophila Groucho, human TLE-1, and a truncated human TLE isoform Amino-enhancer-of-split (AES), work equivalently to repress LEF-1•?-catenin transcription in transient reporter assays, and these actions are sensitive to the HDAC inhibitor Trichostatin A. A survey of Groucho/TLE action in a panel of six colon cancer cell lines with elevated ?-catenin shows that Groucho is not able to repress transcription in a subset of these cell lines. Conclusion Our data shows that Groucho/TLE repression requires two sites of interaction in LEF-1 and that a central, conserved amino acid sequence within the primary region (F S/T/P/xx y I/L/V) is critical. Our data also reveals that AES opposes LEF-1 transcription activation and that both Groucho and AES repression require histone deacetylase activity suggesting multiple steps in Groucho competition with ?-catenin. The variable ability of Groucho/TLE to oppose Wnt signaling in colon cancer cells suggests there may be defects in one or more of these steps.

2009-01-01

124

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

125

Regional nodal failure after conservative surgery and radiotherapy for early-stage breast carcinoma.  

PubMed

We retrospectively analyzed the likelihood of regional nodal failure (RNF) for 1,624 patients with stage I or II invasive breast carcinoma treated with conservative surgery and radiotherapy (RT) at the Joint Center for Radiation Therapy (JCRT) between 1968 and 1985. The median follow-up time was 77 months. RNF was the first site of failure for 38 of the 1,624 patients (2.3%). The incidence of axillary failure for patients undergoing axillary dissection (AXD) who were irradiated to the breast only was 2.1% (nine of 420) for patients with negative nodes and 2.1% (one of 47) for patients with one to three positive nodes. The incidence of supraclavicular failure in these two groups was 1.9% (eight of 420) and 0% (zero of 47), respectively. The incidences of axillary and supraclavicular failure in patients without clinically suspicious axillary involvement who did not have AXD but were treated with RT were 0.8% (three of 355) and 0.3% (one of 364), respectively. Despite various combinations of salvage surgery, RT, and systemic therapy, only 47% of patients (18 of 38) achieved complete regional control after nodal relapse. We conclude that RNF is uncommon in patients treated to the breast alone following an adequate AXD when the axillary nodes are negative or when one to three nodes are positive. RNF is also uncommon in patients with a clinically uninvolved axilla treated with nodal RT without AXD. Symptoms of RNF can be controlled in most but not all patients. Further study is needed to determine if the benefits of RT in preventing a small number of symptomatic RNF outweigh the potential toxicity for any subgroup of patients. PMID:2033433

Recht, A; Pierce, S M; Abner, A; Vicini, F; Osteen, R T; Love, S M; Silver, B; Harris, J R

1991-06-01

126

Conserved cysteine residues in the pore region are obligatory for human TRPM2 channel function.  

PubMed

TRPM2 proteins belong to the melastatin-related transient receptor potential or TRPM subfamily and form Ca(2+)-permeable cationic channels activated by intracellular adenosine diphosphoribose (ADPR). The TRPM2 channel subunit, like all its close relatives, is structurally homologous to the well-characterized voltage-gated potassium channel subunits, each containing six transmembrane segments and a putative pore loop between the fifth and sixth segments. Nevertheless, the structural elements determining the TRPM2 channel functions are still not well understood. In this study, we investigated the functional role of two conserved cysteine residues (at positions 996 and 1008) in the putative pore region of the human TRPM2 by site-directed mutagenesis, combined with electrophysiological and biochemical approaches. Expression of wild-type hTRPM2 channels in human embryonic kidney (HEK-293) cells resulted in robust ADPR-evoked currents. Substitution of cysteine with alanine or serine generated mutant channels that failed to be activated by ADPR. Furthermore, experiments done by Western blot analysis, immunocytochemistry, biotin labeling, and coimmunoprecipitation techniques showed no obvious changes in protein expression, trafficking or membrane localization, and the ability to interact with neighboring subunits that is required for channel assembly. Coexpression of wild-type and mutant subunits significantly reduced the ADPR-evoked currents; for the combination of wild-type and C996S mutant subunits, the reduction was approximately 95%, indicating that incorporation of one or more nonfunctional C996S subunits leads to the loss of channel function. These results taken together suggest that the cysteine residues in the pore region are obligatory for TRPM2 channel function. PMID:16822940

Mei, Zhu-Zhong; Mao, Hong-Ju; Jiang, Lin-Hua

2006-07-05

127

Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes.  

PubMed

Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the Dicistroviridae intergenic region (IGR) are an excellent model system to understand the fundamental tenets of IRES function, requiring no protein factors to manipulate the ribosome and initiate translation. Here, we explore the architecture of four members of the IGR IRESes, representative of the two divergent classes of these IRES RNAs. Using biochemical and structural probing methods, we show that despite sequence variability they contain a common three-dimensional fold. The three-dimensional architecture of the ribosome binding domain from these IRESes is organized around a core helical scaffold, around which the rest of the RNA molecule folds. However, subtle variation in the folds of these IRESes and the presence of an additional secondary structure element suggest differences in the details of their manipulation of the large ribosomal subunit. Overall, the results demonstrate how a conserved three-dimensional RNA fold governs ribosome binding and manipulation. PMID:17544444

Pfingsten, Jennifer S; Costantino, David A; Kieft, Jeffrey S

2007-05-08

128

A novel type of single-stranded nucleic acid binding protein recognizing a highly frequent motif in the intergenic regions of Trypanosoma cruzi  

Microsoft Academic Search

Regulation of gene expression in trypanosomatids is not yet well understood. Genes are organized in long polycistronic transcriptional units separated by intergenic regions that may contain the signaling information for nucleic acid processing. Poly-dinucleotides are frequent in these regions and have been proposed to be involved in regulation of gene expression. Previously, we have reported that [dT–dG] are highly frequent,

Mar??a Ana Duhagon; Bruno Dallagiovanna; Mart??n Ciganda; William Ruyechan; Noreen Williams; Beatriz Garat

2003-01-01

129

The non-conserved region of cucumopine-type Agrobacterium rhizogenes T-DNA is responsible for hairy root induction  

Microsoft Academic Search

The T-DNA regions of three strains of Ri plasmids 1855, 8196, 2659 (agropine, mannopine and cucumopine type respectively) share two highly conserved regions flanking a non-homologous central part [1,2]. We have cloned segments of the cucumopine Ri plasmid 2659 T-DNA in the binary vector system Bin 19 and infected carrot discs with recombinant Agrobacterium strains. We show here that the

M. C. Failla; F. Maimone; A. De Paolis; P. Costantino; M. Cardarelli

1990-01-01

130

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

131

Agricultural Conservation Practices and Wetland Ecosystem Services in a Wetland-Dominated Landscape: The Piedmont-Coastal Plain Region  

Technology Transfer Automated Retrieval System (TEKTRAN)

In the wetlands-rich eastern Coastal Plain and Piedmont region, diverse inland wetlands (riverine, depressional, wet flats) have been impacted by or converted to agriculture. Farm Bill conservation practices that restore or enhance wetlands can return their ecological functions and services to the a...

132

Using occupancy estimation to assess the effectiveness of a regional multiple-species conservation plan: Bats in the Pacific Northwest  

Microsoft Academic Search

Regional conservation plans are increasingly used to plan for and protect biodiversity at large spatial scales however the means of quantitatively evaluating their effectiveness are rarely specified. Multiple-species approaches, particular those which employ site-occupancy estimation, have been proposed as robust and efficient alternatives for assessing the status of wildlife populations over large spatial scales, but implemented examples are few. I

Theodore J. Weller

2008-01-01

133

Membrane order conservation in raft and non-raft regions of hepatocyte plasma membranes from thermally acclimated rainbow trout  

Microsoft Academic Search

Homeoviscous adaptation (HVA), the thermal conservation of membrane fluidity\\/order at different body temperatures, has been observed to varying degrees in different membranes. However, HVA has not been studied in raft and non-raft regions of the plasma membrane (PM) separately. Rafts are ordered PM microdomains implicated in signal transduction, membrane traffic and cholesterol homeostasis. Using infrared spectroscopy, we measured order in

John K Zehmer; Jeffrey R Hazel

2004-01-01

134

CD4+ T Lymphocytes from Calves Immunized with Anaplasma marginale Major Surface Protein 1 (MSP1), a Heteromeric Complex of MSP1a and MSP1b, Preferentially Recognize the MSP1a Carboxyl Terminus That Is Conserved among Strains  

PubMed Central

Native major surface protein 1 (MSP1) of the ehrlichial pathogen Anaplasma marginale induces protective immunity in calves challenged with homologous and heterologous strains. MSP1 is a heteromeric complex of a single MSP1a protein covalently associated with MSP1b polypeptides, of which at least two (designated MSP1F1 and MSP1F3) in the Florida strain are expressed. Immunization with recombinant MSP1a and MSP1b alone or in combination fails to provide protection. The protective immunity in calves immunized with native MSP1 is associated with the development of opsonizing and neutralizing antibodies, but CD4+ T-lymphocyte responses have not been evaluated. CD4+ T lymphocytes participate in protective immunity to ehrlichial pathogens through production of gamma interferon (IFN-?), which promotes switching to high-affinity immunoglobulin G (IgG) and activation of phagocytic cells to produce nitric oxide. Thus, an effective vaccine for A. marginale and related organisms should contain both T- and B-lymphocyte epitopes that induce a strong memory response that can be recalled upon challenge with homologous and heterologous strains. This study was designed to determine the relative contributions of MSP1a and MSP1b proteins, which contain both variant and conserved amino acid sequences, in stimulating memory CD4+ T-lymphocyte responses in calves immunized with native MSP1. Peripheral blood mononuclear cells and CD4+ T-cell lines from MSP1-immunized calves proliferated vigorously in response to the immunizing strain (Florida) and heterologous strains of A. marginale. The conserved MSP1-specific response was preferentially directed to the carboxyl-terminal region of MSP1a, which stimulated high levels of IFN-? production by CD4+ T cells. In contrast, there was either weak or no recognition of MSP1b proteins. Paradoxically, all calves developed high titers of IgG antibodies to both MSP1a and MSP1b polypeptides. These findings suggest that in calves immunized with MSP1 heteromeric complex, MSP1a-specific T lymphocytes may provide help to MSP1b-specific B lymphocytes. The data provide a basis for determining whether selected MSP1a CD4+ T-lymphocyte epitopes and selected MSP1a and MSP1b B-lymphocyte epitopes presented on the same molecule can stimulate a protective immune response.

Brown, Wendy C.; Palmer, Guy H.; Lewin, Harris A.; McGuire, Travis C.

2001-01-01

135

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

PubMed Central

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 charged residues (Arg-9, Glu-79, Arg-82, Lys-86, Asp-163, His-226, Arg-228, Asp-233, Asp-237, Arg-239, Arg-241, Asp-311, Asp-322, and Asp-331) were replaced by alanine. Iodide uptake abilities of mutants were evaluated by steady-state and kinetic analysis. The three-dimensional comparative protein structure of NIS was further modeled using sodium/glucose transporter as the reference protein. Results All the NIS mutants were expressed normally in the cells and targeted correctly to the plasma membrane. However, these mutants, except R9A, displayed severe defects on the iodide uptake. Further kinetic analysis revealed that mutations at conserved positively charged amino acid residues in the extracellular region of NIS led to decrease NIS-mediated iodide uptake activity by reducing the maximal rate of iodide transport, while mutations at conserved negatively charged residues led to decrease iodide transport by increasing dissociation between NIS mutants and iodide. Conclusions This is the first report characterizing thoroughly the functional significance of conserved charged amino acid residues in the extracellular region of NIS. Our data suggested that conserved charged amino acid residues, except Arg-9, in the extracellular region of NIS were critical for iodide transport.

2010-01-01

136

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

137

Recognizing Computational Science  

NASA Astrophysics Data System (ADS)

There are prestigious international awards that recognize the role of theory and experiment in science and mathematics, but there are no awards of a similar stature that explicitly recognize the role of computational science in a scientific field. In 1945, John von Neumann noted that "many branches of both pure and applied mathematics are in great need of computing instruments to break the present stalemate created by the failure of the purely analytical approach to nonlinear problems." In the past few decades, great strides in mathematics and in the applied sciences can be linked to computational science.

Bland-Hawthorn, J.

2006-08-01

138

[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

139

Recognizing complex patterns  

Microsoft Academic Search

How the brain recognizes complex patterns in the environment is a central, but little understood question in neuroscience. The problem is of great significance for a host of applications such as biometric-based access control, autonomous robots and content-based information management. Although some headway in these directions has been made, the current artificial systems do not match the robustness and versatility

Pawan Sinha

2002-01-01

140

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

141

Should recognizers have ears?  

Microsoft Academic Search

Recently, techniques motivated by human auditory perception are being applied in main-stream speech technology and there seems to be renewed interest in implementing more knowledge of human speech communication into a design of a speech recognizer. The paper discusses the author's experience with applying auditory knowledge to automatic recognition of speech. It advances the notion that the reason for applying

Hynek Hermansky

1998-01-01

142

Characterization of Structural Features and Diversity of Variable-Region Determinants of Related Quaternary Epitopes Recognized by Human and Rhesus Macaque Monoclonal Antibodies Possessing Unusually Potent Neutralizing Activities ?  

PubMed Central

A series of potently neutralizing monoclonal antibodies (MAbs) that target quaternary epitopes on the native Env trimer have recently been described. A common feature shared by these antibodies is the critical involvement of sites in both the V2 and V3 variable domains in antibody recognition. In this study the gp120 variable-region determinants were mapped for eight rhesus macaque monoclonal antibodies (RhMAbs) possessing potently neutralizing activity specific for a quaternary target in SF162 Env and compared to those originally identified for human MAb 2909. These studies showed that determinants for the epitopes defined by the RhMAbs differed in both the V2 (positions 160, 167, and 169) and V3 (positions 313 and 315) regions from 2909, and in a number of cases, from each other. Attempts to reconstitute expression of these epitopes on the cell surface by cotransfecting Envs containing either the V2 or the V3 determinant of the epitope were not successful, suggesting that these epitopes were expressed on individual protomers in a trimer-dependent manner. Several of the V2 positions found to be critical for expression of these quaternary epitopes also significantly affected exposure and neutralization sensitivity of targets in the V3 and CD4-binding domains. These results demonstrated a considerable diversity in the fine structure of this class of epitopes and further suggested a potentially important relationship between the expression of such quaternary epitopes and V1/V2-mediated masking of immunodominant epitopes.

Krachmarov, Chavdar; Lai, Zhong; Honnen, William J.; Salomon, Aidy; Gorny, Miroslaw K.; Zolla-Pazner, Susan; Robinson, James; Pinter, Abraham

2011-01-01

143

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

144

THE ECONOMICS OF BIODIVERSITY CONSERVATION-A STUDY IN A COFFEE GROWING REGION OF INDIA  

Microsoft Academic Search

This paper analyses the economics of biodiversity conservation in the context of a tropical ecosystem in India, where coffee is the main competitor for land use.Using primary data covering a cross section of coffee growers,the study notes that the opportunity costs of biodiversity conservation in terms of coffee benefits foregone are quite high.Even after including external costs due to wild

K. N. Ninan; Jyothis Sathyapalan

2003-01-01

145

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

146

Tight junction protein Par6 interacts with an evolutionarily conserved region in the amino terminus of PALS1/stardust.  

PubMed

Tight junctions are the structures in mammalian epithelial cells that separate the apical and basolateral membranes and may also be important in the establishment of cell polarity. Two evolutionarily conserved multiprotein complexes, Crumbs-PALS1 (Stardust)-PATJ and Cdc42-Par6-Par3-atypical protein kinase C, have been implicated in the assembly of tight junctions and in polarization of Drosophila melanogaster epithelia. These two complexes have been linked physically and functionally by an interaction between PALS1 and Par6. Here we identify an evolutionarily conserved region in the amino terminus of PALS1 as the Par6 binding site and identify valine and aspartic acid residues in this region as essential for interacting with the PDZ domain of Par6. We have also characterized, in more detail, the amino terminus of Drosophila Stardust and demonstrate that the interaction mechanism between Stardust and Drosophila Par6 is evolutionarily conserved. Par6 interferes with PATJ in binding PALS1, and these two interactions do not appear to function synergistically. Taken together, these results define the molecular mechanisms linking two conserved polarity complexes. PMID:15140881

Wang, Qian; Hurd, Toby W; Margolis, Ben

2004-05-11

147

Identification of Escherichia coli O157:H7 genomic regions conserved in strains with a genotype associated with human infection.  

PubMed

Beta-glucuronidase-negative, sorbitol-nonfermenting isolates of Shiga toxin-producing Escherichia coli O157 comprise part of a clone complex of related enterohemorrhagic E. coli isolates. High-resolution genotyping shows that the O157 populations have diverged into two different lineages that appear to have different ecologies. To identify genomic regions unique to the most common human-associated genotype, suppression subtractive hybridization was used to identify DNA sequences present in two clinical strains representing the human lineage I O157:H7 strains but absent from two bovine-derived lineage II strains. PCR assays were then used to test for the presence of these regions in 10 lineage I strains and 20 lineage II strains. Twelve conserved regions of genomic difference for lineage I (CRD(I)) were identified that were each present in at least seven of the lineage I strains but absent in most of the lineage II strains tested. The boundaries of the lineage I conserved regions were further delimited by PCR. Eleven of these CRD(I) were associated with E. coli Sakai S-loops 14, 16, 69, 72, 78, 82, 83, 91 to 93, 153, and 286, and the final CRD(I) was located on the pO157 virulence plasmid. Several potential virulence factors were identified within these regions, including a putative hemolysin-activating protein, an iron transport system, and several possible regulatory genes. Cluster analysis based on lineage I conserved regions showed that the presence/absence of these regions was congruent with the inferred phylogeny of the strains. PMID:17056689

Steele, Marina; Ziebell, Kim; Zhang, Yongxiang; Benson, Andrew; Konczy, Paulina; Johnson, Roger; Gannon, Victor

2006-10-20

148

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences  

PubMed Central

Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer.

2010-01-01

149

Recognizing forbidden pleasures  

Microsoft Academic Search

Literary translation is a site of both literary production and ethical engagement. Translators of queer-authored texts ought to recognize how, and to what ends, their subjects use eroticism and desire. English-language translators have had varied successes in such recognition of how twentieth-century Spanish poet Luis Cernuda himself constructs the social, ethical and poetic importance of desire and passion. Depending on

Eric Keenaghan

2011-01-01

150

Is the conserved mammalian region of ZNF804A locus associated with schizophrenia? A population-based genetics analysis  

Microsoft Academic Search

Recently, several genome-wide association studies (GWASs) have reproduced the significant association of the single nucleotide polymorphism (SNP) rs1344706 (located in intron 2 of the zinc finger protein 804A (ZNF804A) on chromosome 2q32.1) with schizophrenia. Bioinformatic analysis of the chromosome segment around rs1344706 suggests that a short conserved mammalian region exists approximately 3kb downstream of rs1344706. In the present work, we

Rui Zhang; Robert K. Valenzuela; Shemin Lu; Liesu Meng; Tingwei Guo; Xiaoyun Du; Wanhu Kang; Jie Ma

151

A landscape approach to conserving wetland bird habitat in the Prairie Pothole Region of eastern South Dakota  

Microsoft Academic Search

Resource managers confronted with preserving ecosystems for prairie wetland birds in fragmented landscapes require landscape\\u000a studies that direct conservation efforts over broad geographic regions. We investigated the role of local and landscape factors\\u000a affecting habitat suitability by integrating remotely sensed wetland and land-cover data with wetland bird habitat models.\\u000a We linked habitat models with locations of easement and fee-title wetlands

David E. Naugle; Rex R. Johnson; Michael E. Estey; Kenneth F. Higgins

2000-01-01

152

A landscape approach to conserving wetland bird habitat in the prairie pothole region of eastern South Dakota  

Microsoft Academic Search

Resource managers confronted with preserving ecosystems for prairie wetland birds in fragmented landscapes require landscape\\u000a studies that direct conservation efforts over broad geographic regions. We investigated the role of local and landscape factors\\u000a affecting habitat suitability by integrating remotely sensed wetland and land-cover data with wetland bird habitat models.\\u000a We linked habitat models with locations of easement and fee-title wetlands

David E. Naugle; Rex R. Johnson; Michael E. Estey; Kenneth F. Higgins

2001-01-01

153

A Regional Assessment of the Effects of Conservation Practices on In-stream Water Quality  

NASA Astrophysics Data System (ADS)

The Conservation Effects Assessment Program (CEAP), initiated by USDA Natural Resources Conservation Service (NRCS), has the goal of quantifying the environmental benefits of agricultural conservation practices. As part of this effort, detailed farmer surveys were compiled to document the adoption of conservation practices. Survey data showed that up to 38 percent of cropland in the Upper Mississippi River basin is managed to reduce sediment, nutrient and pesticide loads from agricultural activities. The broader effects of these practices on downstream water quality are challenging to quantify. The USDA-NRCS recently reported results of a study that combined farmer surveys with process-based models to deduce the effect of conservation practices on sediment and chemical loads in farm runoff and downstream waters. As a follow-up collaboration, USGS and USDA scientists conducted a semi-empirical assessment of the same suite of practices using the USGS SPARROW (SPAtially Referenced Regression On Watershed attributes) modeling framework. SPARROW is a hybrid statistical and mechanistic stream water quality model of annual conditions that has been used extensively in studies of nutrient sources and delivery. In this assessment, the USDA simulations of the effects of conservation practices on loads in farm runoff were used as an explanatory variable (i.e., change in farm loads per unit area) in a component of an existing a SPARROW model of the Upper Midwest. The model was then re-calibrated and tested to determine whether the USDA estimate of conservation adoption intensity explained a statistically significant proportion of the spatial variability in stream nutrient loads in the Upper Mississippi River basin. The results showed that the suite of conservation practices that NRCS has catalogued as complete nutrient and sediment management are a statistically significant feature in the Midwestern landscape associated with phosphorous runoff and delivery to downstream waters. Effects on the delivery of nitrogen will be also be studied. Estimates of the magnitude of this effect using SPARROW indicated that phosphorus load reductions ranged from about 2 - 38% for various spatial scales. This is less than reported by the USDA CEAP simulations, which ranged from 15 - 49%. Nevertheless, the results indicated that conservation practices play a significant role in reducing phosphorus pollution from agricultural activities to downstream receiving water bodies.

Garcia, A. M.; Alexander, R. B.; Arnold, J.; Norfleet, L.; Robertson, D. M.; White, M.

2011-12-01

154

Is the conserved mammalian region of ZNF804A locus associated with schizophrenia? A population-based genetics analysis.  

PubMed

Recently, several genome-wide association studies (GWASs) have reproduced the significant association of the single nucleotide polymorphism (SNP) rs1344706 (located in intron 2 of the zinc finger protein 804A (ZNF804A) on chromosome 2q32.1) with schizophrenia. Bioinformatic analysis of the chromosome segment around rs1344706 suggests that a short conserved mammalian region exists approximately 3kb downstream of rs1344706. In the present work, we studied all SNPs in this conserved mammalian region and performed genetic analyses on samples from Chinese schizophrenia patients (n = 516) and compared control subjects (n = 520). Significant association between an allele of rs13423388 and schizophrenia was found (P = 0.0012). Haplotype analysis of the three SNPs rs4666998, rs13423388, and rs56280129 showed significant associations with schizophrenia (global P = 0.00001). Furthermore, we performed a four-SNP haplotype analysis which included the SNPs from the three-SNP haplotype analysis and rs1344706 (global P = 0.0005), and found that haplotype GCCG was associated with schizophrenia (P = 0.003). In summary, the present study adds new evidence for an association between the conserved mammalian region of the ZNF804A gene and schizophrenia. Further research is needed to clarify the transcriptional regulation of ZNF804A gene and to relate this to the pathophysiology of schizophrenia. PMID:21993378

Zhang, Rui; Valenzuela, Robert K; Lu, Shemin; Meng, Liesu; Guo, Tingwei; Du, Xiaoyun; Kang, Wanhu; Ma, Jie

2011-10-12

155

A conserved proline-rich region of the Saccharomyces cerevisiae cyclase-associated protein binds SH3 domains and modulates cytoskeletal localization.  

PubMed

Saccharomyces cerevisiae cyclase-associated protein (CAP or Srv2p) is multifunctional. The N-terminal third of CAP binds to adenylyl cyclase and has been implicated in adenylyl cyclase activation in vivo. The widely conserved C-terminal domain of CAP binds to monomeric actin and serves an important cytoskeletal regulatory function in vivo. In addition, all CAP homologs contain a centrally located proline-rich region which has no previously identified function. Recently, SH3 (Src homology 3) domains were shown to bind to proline-rich regions of proteins. Here we report that the proline-rich region of CAP is recognized by the SH3 domains of several proteins, including the yeast actin-associated protein Abp1p. Immunolocalization experiments demonstrate that CAP colocalizes with cortical actin-containing structures in vivo and that a region of CAP containing the SH3 domain binding site is required for this localization. We also demonstrate that the SH3 domain of yeast Abp1p and that of the yeast RAS protein guanine nucleotide exchange factor Cdc25p complex with adenylyl cyclase in vitro. Interestingly, the binding of the Cdc25p SH3 domain is not mediated by CAP and therefore may involve direct binding to adenylyl cyclase or to an unidentified protein which complexes with adenylyl cyclase. We also found that CAP homologous from Schizosaccharomyces pombe and humans bind SH3 domains. The human protein binds most strongly to the SH3 domain from the abl proto-oncogene. These observations identify CAP as an SH3 domain-binding protein and suggest that CAP mediates interactions between SH3 domain proteins and monomeric actin. PMID:8552082

Freeman, N L; Lila, T; Mintzer, K A; Chen, Z; Pahk, A J; Ren, R; Drubin, D G; Field, J

1996-02-01

156

Changing perspectives on biodiversity conservation: from species protec- tion to regional sustainability  

Microsoft Academic Search

Biodiversity is the basis for ecosystem goods and services that provide for human survival and prosperity. With a rapidly increasing human population and its demands for natural resources, landscapes are being fragmented, habitats are being destroyed, and biodiversity is declining. How can biodiversity be effec- tively conserved in the face of increasing human pressures? In this paper, I review changing

Jianguo Wu

2008-01-01

157

LANDSCAPE CONSERVATION AND ECONOMIC INTERDEPENDENCE: A CASESTUDY OF WELSH NATIONAL PARKS AND THE REGIONAL ECONOMY  

Microsoft Academic Search

Conservation of the cherished landscapes of National Parks in Britain takes place around the communities which inhabit them. Economic activities of their populations are subject to both constraints and opportunities which the statutory protection provides, with much of the development of economies displaced into their hinterlands. Analysis of spatial relationships between the three National Parks of Wales and the rest

Peter Midmore

2008-01-01

158

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

159

Local and regional-scale societal dynamics in grizzly bear conservation  

Microsoft Academic Search

Conserving grizzly bear populations is a significant challenge for wildlife managers throughout North America. Much fruitful research has been conducted on the biology of grizzlies, but the human dimensions of bear management remain poorly understood. This imbalance has created conflicts between management agencies and local inhabitants that can jeopardize ecosystem management and planning programs in which grizzlies often feature as

Douglas Andrew Clark

2007-01-01

160

Conservation Tillage as a Solution to Drought in Both the Southeastern and Western Peanut Growing Regions  

Technology Transfer Automated Retrieval System (TEKTRAN)

Conservation tillage cropping systems were introduced in the 1970s and much research has documented positive benefits such as decreased erosion, general soil improvement (carbon sequestration), and decreased labor, time, and fuel devoted to land preparation. Strip tillage, in-row subsoiling followe...

161

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

162

Conservation of Babesia bovis Small Heat Shock Protein (Hsp20) among Strains and Definition of T Helper Cell Epitopes Recognized by Cattle with Diverse Major Histocompatibility Complex Class II Haplotypes  

Microsoft Academic Search

Babesia bovis small heat shock protein (Hsp20) is recognized by CD4 T lymphocytes from cattle that have recovered from infection and are immune to challenge. This candidate vaccine antigen is related to a protective antigen of Toxoplasma gondii, Hsp30\\/bag1, and both are members of the -crystallin family of proteins that can serve as molecular chaperones. In the present study, immunofluorescence

Junzo Norimine; Juan Mosqueda; Guy H. Palmer; Harris A. Lewin; Wendy C. Brown

2004-01-01

163

Structural analysis of the 5{prime} region of mouse and human Huntington disease genes reveals conservation of putative promoter region and Di- and trinucleotide polymorphisms  

SciTech Connect

We have previously cloned and characterized the murine homologue of the Huntington disease (HD) gene and shown that it maps to mouse chromosome 5 within a region of conserved synteny with human chromosome 4p16.3. Here we present a detailed comparison of the sequence of the putative promoter and the organization of the 5{prime} genomic region of the murine (Hdh) and human HD genes encompassing the first five exons. We show that in this region these two genes share identical exon boundaries, but have different-size introns. Two dinucleotide (CT) and one trinucleotide intronic polymorphism in Hdh and an intronic CA polymorphism in the HD gene were identified. Comparison of 940-bp sequence 5{prime} to the putative translation start site reveals a highly conserved region (78.8% nucleotide identity) between Hdh and the HD gene from nucleotide -56 to -206 (of Hdh). Neither Hdh nor the HD gene have typical TATA or CCAAT elements, but both show one putative AP2 binding site and numerous potential Sp1 binding sites. The high sequence identity between Hdh and the HD gene for approximately 200 bp 5{prime} to the putative translation start site indicates that these sequences may play a role in regulating expression of the Huntington disease gene. 30 refs., 4 figs., 2 tabs.

Lin, Biaoyang; Nasir, J.; Kalchman, M.A. [Univ. of British Columbia, Vancouver, Britsh Columbia (Canada)] [and others

1995-02-10

164

Identification of mouse adenovirus type 1 early region 1: DNA sequence and a conserved transactivating function.  

PubMed Central

The left end of the genome of mouse adenovirus type 1 (also known as strain FL) was characterized by determination of the DNA sequence, amino acid similarities with early region proteins of primate adenoviruses, and a functional assay. Several specific DNA sequence features were similar to those found in human adenoviruses, and open reading frames from this region could encode proteins similar to human adenovirus early region 1A and early region 1B proteins. DNAs from this region were tested in transient-expression assays in human and mouse cells were found to transactivate the human adenovirus type 5 early region 3 promoter fused to the chloramphenicol acetyltransferase gene. The data indicate structural and functional homologies between mouse adenovirus type 1 early region 1 and early region 1 of primate adenoviruses. Images

Ball, A O; Williams, M E; Spindler, K R

1988-01-01

165

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments  

PubMed Central

Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

Ajawatanawong, Pravech; Atkinson, Gemma C.; Watson-Haigh, Nathan S.; MacKenzie, Bryony; Baldauf, Sandra L.

2012-01-01

166

Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris).  

PubMed

We sequenced the entire control region and portions of flanking genes (tRNA(Phe), tRNA(Glu), and ND6) in the common chaffinch (Fringilla coelebs), blue chaffinch (F. teydea), brambling (F. montifringilla), and greenfinch (Carduelis chloris). In these finches the control region is similar in length (1,223-1,237 bp) and has the same flanking gene order as in other birds, and contains a putative TAS element and the highly conserved CSB-1 and F, D, and C boxes recognizable in most vertebrates. Cloverleaf-like structures associated with the TAS element at the 5' end and CSB-1 at the 3' end of the control region may be involved with the stop and start of D-loop synthesis, respectively. The pattern of nucleotide and substitution bias is similar to that in other vertebrates, and consequently the finch control region can be subdivided into a central, conserved G-rich domain (domain II) flanked by hypervariable 5'-C-rich (domain I) and 3'-AT-rich (domain III) segments. In pairwise comparisons among finch species, the central domain has unusually low transition/transversion ratios, which suggests that increased G + T content is a functional constraint, possibly for DNA primase efficiency. In finches the relative rates of evolution vary among domains according to a ratio of 4.2 (domain III) to 2.2 (domain I) to 1 (domain II), and extensively among sites within domains I and II. Domain I and III sequences are extremely useful in recovering intraspecific phylogeographic splits between populations in Africa and Europe, Madeira, and a basal lineage in Nefza, Tunisia. Domain II sequences are highly conserved, and are therefore only useful in conjunction with sequences from domains I and III in phylogenetic studies of closely related species. PMID:9029795

Marshall, H D; Baker, A J

1997-02-01

167

Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.  

PubMed

Sequences from the 5' region of R2 retrotransposons of four species of silk moth are reported. In Bombyx mori, this region of the R2 messenger RNA contains a binding site for R2 protein and mediates interactions critical to R2 element insertion into the host genome. A model of secondary structure for a segment of this RNA is proposed on the basis of binding to oligonucleotide microarrays, chemical mapping, and comparative sequence analysis. Five conserved secondary structures are identified, including a novel pseudoknot. There is an apparent transition from an entirely RNA structure coding function in most of the 5' segment to a protein coding function near the 3' end. This suggests that local regions evolved under separate functional constraints (structural, coding, or both). PMID:19397915

Kierzek, Elzbieta; Christensen, Shawn M; Eickbush, Thomas H; Kierzek, Ryszard; Turner, Douglas H; Moss, Walter N

2009-05-03

168

Possible conservation units of the sun bear (Helarctos malayanus) in Sarawak based on variation of mtDNA control region.  

PubMed

The mitochondrial DNA control region of the sun bear (Helarctos malayanus) was sequenced using 21 DNA samples collected from confiscated sun bears to identify conservation units, such as evolutionarily significant units and management units, in Sarawak, Borneo Island. A total of 10 haplotypes were observed, indicating the presence of at least two lineages in the sun bear population in Sarawak. Presumably, these two lineages could represent evolutionarily significant units. However, the geographical distributions of the two lineages remained unknown due to the lack of information regarding the exact capture locations of the confiscated sun bears. It is essential to elucidate the geographical distributions of these lineages in order to create a proper conservation plan for the sun bears in Sarawak. Therefore, further studies examining the haplotype distributions using DNA samples from known localities are essential. PMID:17201199

Onuma, Manabu; Suzuki, Masatsugu; Ohtaishi, Noriyuki

2006-11-01

169

Potential conservation opportunities from the use of improved irrigation scheduling in the Pacific Northwest region  

SciTech Connect

This report documents research to identify the potential energy savings and the costs per kWh saved from using systematic rather than traditional irrigation scheduling to reduce water usage in the irrigated agricultural sector of the Pacific Northwest. This research is part of an overall project aimed at developing a computer model and data base that will allow for estimation of the potential energy savings and cost effectiveness of a number of conservation technologies that are available for use in irrigated agriculture.

Harrer, B J; Lezberg, A J

1985-03-01

170

A Water Quality Model for Regional Stream Assessment and Conservation Strategy Development  

Microsoft Academic Search

Non-point-source (NPS) pollution remains the primary source of stream impairment in the United States. Many problems such\\u000a as eutrophication, sedimentation, and hypoxia are linked with NPS pollution which reduces the water quality for aquatic and\\u000a terrestrial organisms. Increasingly, NPS pollution models have been used for landscape-scale pollution assessment and conservation\\u000a strategy development. Our modeling approach functions at a scale between

Marcia S. Meixler; Mark B. Bain

2010-01-01

171

Modelling the impacts of payments for biodiversity conservation on regional land-use patterns  

Microsoft Academic Search

We present a land-use allocation model that evaluates the impact of payments for ecosystem services such as biodiversity conservation on land-use patterns. In a non-linear optimisation procedure, land use is allocated at farm level, taking into account risk behaviour, and spatial as well as temporal variability of net revenues of land-use alternatives, using a spatial resolution of 29m×29m. The model

G. H. J. de Koning; P. C. Benítez; F. Muńoz; R. Olschewski

2007-01-01

172

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

173

Viral envelope protein folding and membrane hemifusion are enhanced by the conserved loop region of HIV-1 gp41  

PubMed Central

Fusion of human immunodeficiency virus (HIV-1) with target cells is mediated by the gp41 transmembrane envelope protein. The loop region within gp41 contains 2 crucial cysteines that play an unknown role in HIV-cell fusion. On the basis of cell-cell fusion assay, using human T-cell lines [Jurkat E6-1 and Jurkat HXBc2(4)], and virus-cell fusion assay, using fully infectious HIV-1 HXBc2 virus and TZM-bl human cell line, we provide evidence that the oxidation state of the disulfide bond within a loop domain peptide determines its activity. The oxidized (closed) form inhibits fusion, while the reduced (opened) form enhances hemifusion. These opposite activities reach 60% difference in viral fusion. Both forms of the loop domain interact with gp41: the opened form enhances gp41 folding into a bundle, whereas the closed form inhibits this folding. Therefore, the transformation of the cysteines from a reduced to an oxidized state enables the loop to convert from opened to closed conformations, which assists gp41 to fold and induces hemifusion. The significant conservation of the loop region within many envelope proteins suggests a general mechanism, which is exploited by viruses to enhance entry into their host cells.—Ashkenazi, A., Viard, M., Wexler-Cohen, Y., Blumenthal, R., Shai, Y. Viral envelope protein folding and membrane hemifusion are enhanced by the conserved loop region of HIV-1 gp41.

Ashkenazi, Avraham; Viard, Mathias; Wexler-Cohen, Yael; Blumenthal, Robert; Shai, Yechiel

2011-01-01

174

Integrated assessment of conservation opportunities in the irrigated agriculture sector of the Pacific Northwest Region  

SciTech Connect

This report documents research to identify the potential energy savings and cost per kWh saved for implementing currently available energy conservation measures in the irrigated agriculture sector of the Pacific Northwest. A computer model that simulates the energy consumption process of irrigation systems and estimates the levelized costs of undertaking conservation investments is the primary analytical tool used in this research. Using engineering and economic input parameters for the various conservation measures that could potentially be implemented in irrigated agriculture, the Irrigation Sector Energy Planning (ISEP) model generates estimates of energy savings and cost per kWh saved for the measures. All parameters input to the ISEP model are based upon empirical field data. Results provided by the ISEP model indicate tht by the year 2003 a total of approximately 158.6 average MW of energy could potentially be saved in the Pacific Northwest irrigation sector on all sprinkler-irrigated acres. Approximately 130.4 average MW can be saved on acres currently by sprinkler, while an additional 28.2 average MW could be saved on new acres that are forecast to come under irrigation in the next 20 years. The largest share of the total savings (47%) is estimated to come from the use of low-pressure irrigation. Over 60% of the total potential savings 158.6 average MW is estimated to be available for a cost per kWh saved of 20 mills or less and over 75% could be achieved for a cost of 30 mills or less. Savings from low-pressure irrigation and the redesign of fittings and mainlines will normally cost less than 20 mills per kWh saved. Almost all of the savings that are estimated to cost more than 30 mills per kWh saved to obtain are savings from improved irrigation scheduling on irrigated acres that use surface water and have low average pumping lifts.

Harrer, B.J.; Lezberg, A.J.; Wilfert, G.L.

1985-02-01

175

Cotton production potential and water conservation impact using the regional irrigation demand model of northern Texas  

Technology Transfer Automated Retrieval System (TEKTRAN)

Revised irrigation demands are calculated for the 21 northernmost counties in Texas, identified as Panhandle Region (also known as Region A), using the TAMA (Texas A&M–Amarillo) agricultural water use demand estimation model. Year 2000 demands are presented using the existing mixture of crops, aver...

176

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

Microsoft Academic Search

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

M ANGEL

1987-01-01

177

Monoclonal Antibody 11E10, Which Neutralizes Shiga Toxin Type 2 (Stx2), Recognizes Three Regions on the Stx2 A Subunit, Blocks the Enzymatic Action of the Toxin In Vitro, and Alters the Overall Cellular Distribution of the Toxin?  

PubMed Central

Monoclonal antibody (MAb) 11E10 recognizes the Shiga toxin type 2 (Stx2) A1 subunit. The binding of 11E10 to Stx2 neutralizes both the cytotoxic and lethal activities of Stx2, but the MAb does not bind to or neutralize Stx1 despite the 61% identity and 75% similarity in the amino acids of the A1 fragments. In this study, we sought to identify the segment or segments on Stx2 that constitute the 11E10 epitope and to determine how recognition of that region by 11E10 leads to inactivation of the toxin. Toward those objectives, we generated a set of chimeric Stx1/Stx2 molecules and then evaluated the capacity of 11E10 to recognize those hybrid toxins by Western blot analyses and to neutralize them in Vero cell cytotoxicity assays. We also compared the amino acid sequences and crystal structures of Stx1 and Stx2 for stretches of dissimilarity that might predict a binding epitope on Stx2 for 11E10. Through these assessments, we concluded that the 11E10 epitope is comprised of three noncontiguous regions surrounding the Stx2 active site. To determine how 11E10 neutralizes Stx2, we examined the capacity of 11E10/Stx2 complexes to target ribosomes. We found that the binding of 11E10 to Stx2 prevented the toxin from inhibiting protein synthesis in an in vitro assay but also altered the overall cellular distribution of Stx2 in Vero cells. We propose that the binding of MAb 11E10 to Stx2 neutralizes the effects of the toxin by preventing the toxin from reaching and/or inactivating the ribosomes.

Smith, Michael J.; Melton-Celsa, Angela R.; Sinclair, James F.; Carvalho, Humberto M.; Robinson, Cory M.; O'Brien, Alison D.

2009-01-01

178

CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes  

PubMed Central

Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elements responsible for specific patterns of transcriptional regulation represents a critical area of investigation. Computational methods for the identification of functional cis-regulatory modules are difficult to devise, principally because of the short length and degenerate nature of individual cis-element binding sites and the inherent complexity that is generated by combinatorial interactions within cis-clusters. Filtering candidate cis-element clusters based on phylogenetic conservation is helpful for an individual ortholog gene pair, but combining data from cis-conservation and coordinate expression across multiple genes is a more difficult problem. To approach this, we have extended an ortholog gene-pair database with additional analytical architecture to allow for the analysis and identification of maximal numbers of compositionally similar and phylogenetically conserved cis-regulatory element clusters from a list of user-selected genes. The system has been successfully tested with a series of functionally related and microarray profile-based co-expressed ortholog pairs of promoters and genes using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets. CisMols Analyzer is accessible via a Web interface at .

Jegga, Anil G.; Gupta, Ashima; Gowrisankar, Sivakumar; Deshmukh, Mrunal A.; Connolly, Steven; Finley, Kevin; Aronow, Bruce J.

2005-01-01

179

CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes.  

PubMed

Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elements responsible for specific patterns of transcriptional regulation represents a critical area of investigation. Computational methods for the identification of functional cis-regulatory modules are difficult to devise, principally because of the short length and degenerate nature of individual cis-element binding sites and the inherent complexity that is generated by combinatorial interactions within cis-clusters. Filtering candidate cis-element clusters based on phylogenetic conservation is helpful for an individual ortholog gene pair, but combining data from cis-conservation and coordinate expression across multiple genes is a more difficult problem. To approach this, we have extended an ortholog gene-pair database with additional analytical architecture to allow for the analysis and identification of maximal numbers of compositionally similar and phylogenetically conserved cis-regulatory element clusters from a list of user-selected genes. The system has been successfully tested with a series of functionally related and microarray profile-based co-expressed ortholog pairs of promoters and genes using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets. CisMols Analyzer is accessible via a Web interface at http://cismols.cchmc.org/. PMID:15980500

Jegga, Anil G; Gupta, Ashima; Gowrisankar, Sivakumar; Deshmukh, Mrunal A; Connolly, Steven; Finley, Kevin; Aronow, Bruce J

2005-07-01

180

Conservation of socioculturally important local crop biodiversity in the Oromia region of Ethiopia: a case study.  

PubMed

In this study, we surveyed diversity in a range of local crops in the Lume and Gimbichu districts of Ethiopia, together with the knowledge of local people regarding crop uses, socio-economic importance, conservation, management and existing threats. Data were collected using semistructured interviews and participant observation. The study identified 28 farmers' varieties of 12 crop species. Among these, wheat (Triticum turgidum) and tef (Eragrostis tef) have high intra-specific diversity, with 9 and 6 varieties respectively. Self-seed supply or seed saving was the main (80 %) source of seeds for replanting. Agronomic performance (yield and pest resistance), market demand, nutritional and use diversity attributes of the crop varieties were highlighted as important criteria for making decisions regarding planting and maintenance. Over 74 % of the informants grow a combination of "improved" and farmers' varieties. Of the farmers' varieties, the most obvious decline and/or loss was reported for wheat varieties. Introduction of improved wheat varieties, pest infestation, shortage of land, low yield performance and climate variability were identified as the principal factors contributing to this loss or decline. Appropriate interventions for future conservation and sustainable use of farmers' varieties were suggested. PMID:22729809

Balemie, Kebu; Singh, Ranjay K

2012-06-24

181

Conservation of Socioculturally Important Local Crop Biodiversity in the Oromia Region of Ethiopia: A Case Study  

NASA Astrophysics Data System (ADS)

In this study, we surveyed diversity in a range of local crops in the Lume and Gimbichu districts of Ethiopia, together with the knowledge of local people regarding crop uses, socio-economic importance, conservation, management and existing threats. Data were collected using semistructured interviews and participant observation. The study identified 28 farmers' varieties of 12 crop species. Among these, wheat ( Triticum turgidum) and tef ( Eragrostis tef) have high intra-specific diversity, with 9 and 6 varieties respectively. Self-seed supply or seed saving was the main (80 %) source of seeds for replanting. Agronomic performance (yield and pest resistance), market demand, nutritional and use diversity attributes of the crop varieties were highlighted as important criteria for making decisions regarding planting and maintenance. Over 74 % of the informants grow a combination of "improved" and farmers' varieties. Of the farmers' varieties, the most obvious decline and/or loss was reported for wheat varieties. Introduction of improved wheat varieties, pest infestation, shortage of land, low yield performance and climate variability were identified as the principal factors contributing to this loss or decline. Appropriate interventions for future conservation and sustainable use of farmers' varieties were suggested.

Balemie, Kebu; Singh, Ranjay K.

2012-09-01

182

Conserved Regions from Neisseria gonorrhoeae Pilin Are Immunosilent and Not Immunosuppressive  

Microsoft Academic Search

PilE is the primary subunit of type IV pili from Neisseria gonorrhoeae and contains a surface-exposed hypervariable region thought to be one feature of pili that has prevented development of a pilin-based vaccine. We have created a three-dimensional structure-based antigen by replacing the hypervariable region of PilE with an aspartate-glutamine linker chosen from the sequence of Pseudomonas aeruginosa PilA. We

Johanna K. Hansen; Karen P. Demick; John M. Mansfield; Katrina T. Forest

2007-01-01

183

Conservative mutations in the immunosuppressive region of the bovine leukemia virus transmembrane protein affect fusion but not infectivity in vivo.  

PubMed

Many retroviruses, including bovine leukemia virus (BLV), contain a highly conserved region located about 40 amino acids downstream from the fusion peptide within the sequence of the external domain of the transmembrane (TM) protein. This region is notably thought to be involved in the presentation of the NH2-terminal peptide to allow cell fusion. By using hydrophobic cluster analysis and by analogy with the influenza A hemagglutinin structures, the core of the TM structure including this particular region was predicted to consist, in the BLV and other retroviral envelope proteins, of an alpha-helix followed by a loop region, both docked against a subsequent alpha-helix that forms a triple-stranded coiled coil. The loop region could undergo, as in hemagglutinin, a major refolding into an alpha-helix integrating the coiled coil structure and putting the fusion peptide to one tip of the molecule. Based on this model, we have identified amino acids that may be essential to the BLV TM structure, and a series of mutations were introduced in the BLV env gene of an infectious molecular clone. A first series of mutations was designed to disturb the coiled coil structure (substitutions with proline residues), whereas others would maintain the general TM structure. When expressed by Semliki Forest virus recombinants, all the mutated envelope proteins were stable and efficiently synthesized in baby hamster kidney cells. Both proline-substituted and conservative mutants were strongly affected in their capacity to fuse to CC81 indicator cells. In addition, it appeared that the integrity of the TM coiled coil structure is essential for envelope protein multimerization, as analyzed by metrizamide gradient centrifugation. Finally, to gain insight into the role of this coiled coil in the infectious potential of BLV in vivo, the mutated TM genes were introduced in an infectious and pathogenic molecular clone and injected into sheep. It appeared that only the conservative mutations (A60V and A64S) allowed maintenance of viral infectivity in vivo. Since these mutations destroyed the ability to induce syncytia, we conclude that efficient fusion capacity of the recombinant envelopes is not a prerequisite for the infectious potential of BLV in vivo. Viral propagation of these mutants was strongly affected in some of the infected sheep. However, the proviral loads within half of the infected animals (2 out of 2 for A60V and 1 out of 4 for A64S) were close to the wild-type levels. In these sheep, it thus appears that the A60V and A64S mutants propagate efficiently despite being unable to induce syncytia in cell culture. PMID:9582317

Gatot, J S; Callebaut, I; Mornon, J P; Portetelle, D; Burny, A; Kerkhofs, P; Kettmann, R; Willems, L

1998-05-22

184

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

185

Phylogenetic Footprinting Reveals Evolutionarily Conserved Regions of the Gonadotropin-Releasing Hormone Gene that Enhance Cell-Specific Expression  

PubMed Central

Reproductive function is controlled by the hypothalamic neuropeptide, GnRH, which serves as the central regulator of the hypothalamic-pituitary-gonadal axis. GnRH expression is limited to a small population of neurons in the hypothalamus. Targeting this minute population of neurons (as few as 800 in the mouse) requires regulatory elements upstream of the GnRH gene that remain to be fully characterized. Previously, we have identified an evolutionarily conserved promoter region (?173 to ?1) and an enhancer (?1863 to ?1571) in the rat gene that targets a subset of the GnRH neurons in vivo. In the present study, we used phylogenetic sequence comparison between human and rodents and analysis of the transcription factor clusters within conserved regions in an attempt to identify additional upstream regulatory elements. This approach led to the characterization of a new upstream enhancer that regulates expression of GnRH in a cell-specific manner. Within this upstream enhancer are nine binding sites for Octamer-binding transcription factor 1 (OCT1), known to be an important transcriptional regulator of GnRH gene expression. In addition, we have identified nuclear factor I (NF1) binding to multiple elements in the GnRH-regulatory regions, each in close proximity to OCT1. We show that OCT1 and NF1 physically and functionally interact. Moreover, the OCT1 and NF1 binding sites in the regulatory regions appear to be essential for appropriate GnRH gene expression. These findings indicate a role for this upstream enhancer and novel OCT1/NF1 complexes in neuron-restricted expression of the GnRH gene.

GIVENS, MARJORY L.; KUROTANI, REIKO; RAVE-HAREL, NAAMA; MILLER, NICHOL L. G.; MELLON, PAMELA L.

2010-01-01

186

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

2013-02-06

187

The fully conserved Asp residue in conserved sequence region I of the ?-amylase family is crucial for the catalytic site architecture and activity  

Microsoft Academic Search

The ?-amylase family is a large group of starch processing enzymes [Svensson, B. (1994) Plant Mol. Biol. 25, 141–157]. It is characterized by four short sequence motifs that contain the seven fully conserved amino acid residues in this family: two catalytic carboxylic acid residues and four substrate binding residues. The seventh conserved residue (Asp135) has no direct interactions with either

Hans Leemhuis; Henriëtte J. Rozeboom; Bauke W. Dijkstra; Lubbert Dijkhuizen

2003-01-01

188

Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates  

PubMed Central

Here, we report the characterization of 122 Pseudomonas aeruginosa clinical isolates from three distinct geographical locations: Dartmouth Hitchcock Medical Center in New Hampshire, USA, the Charles T. Campbell Eye Microbiology Lab at the University of Pittsburgh Medical Center, USA, and the Aravind Eye Hospital in Madurai, India. We identified and located clustered regularly interspaced short palindromic repeats (CRISPR) in 45/122 clinical isolates and sequenced these CRISPR, finding that Yersinia subtype CRISPR regions (33?%) were more prevalent than the Escherichia CRISPR region subtype (6?%) in these P. aeruginosa clinical isolates. Further, we observed 132 unique spacers from these 45 CRISPR that are 100?% identical to prophages or sequenced temperate bacteriophage capable of becoming prophages. Most intriguingly, all of these 132 viral spacers matched to temperate bacteriophage/prophages capable of inserting into the host chromosome, but not to extrachromosomally replicating lytic P. aeruginosa bacteriophage. We next assessed the ability of the more prevalent Yersinia subtype CRISPR regions to mediate resistance to bacteriophage infection or lysogeny by deleting the entire CRISPR region from sequenced strain UCBPP-PA14 and six clinical isolates. We found no change in CRISPR-mediated resistance to bacteriophage infection or lysogeny rate even for CRISPR with spacers 100?% identical to a region of the infecting bacteriophage. Lastly, to show these CRISPR and cas genes were expressed and functional, we demonstrated production of small CRISPR RNAs. This work provides both the first examination to our knowledge of CRISPR regions within clinical P. aeruginosa isolates and a collection of defined CRISPR-positive and -negative strains for further CRISPR and cas gene studies.

Cady, K. C.; White, A. S.; Hammond, J. H.; Abendroth, M. D.; Karthikeyan, R. S. G.; Lalitha, P.; Zegans, M. E.; O'Toole, G. A.

2011-01-01

189

Energy Use and Conservation in the Residential Sector: A Regional Analysis.  

National Technical Information Service (NTIS)

The report estimates consumption of energy in the residential sector, broken down by the major end uses, for each of the nine census regions of the United States for the base year 1970. A forecasting methodology based in part on econometrics makes project...

S. H. Dole

1975-01-01

190

Cotton production potential and water conservation impact using the regional irrigation demand model of northern Texas  

Microsoft Academic Search

Revised irrigation demands are calculated for the 21 northernmost counties in Texas, identified as Region A, using the TAMA (Texas A&M-Amarillo) agricultural water use demand estimation model. Year 2000 demands are presented using the existing mixture of crops, average evapotranspiration values and actual irrigation application practice values. Current demand values are expected to exceed the allowable water supply in several,

Thomas Marek; Dana Porter; Terry Howell; Prasanna Gowda; Paul Colaizzi

191

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies  

PubMed Central

Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC) and H. melpomene (Yb-linked BAC) revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved over very long evolutionary time scales. Conclusion Here we have demonstrated the tractability of progressing from a genetic linkage map to genomic sequence data in Heliconius butterflies. We have also shown that fine-scale gene order is highly conserved between distantly related Heliconius species, and also between Heliconius and B. mori. Together, these findings suggest that genome structure in macrolepidoptera might be very conserved, and show that mapping and positional cloning efforts in different lepidopteran species can be reciprocally informative.

Papa, Riccardo; Morrison, Clayton M; Walters, James R; Counterman, Brian A; Chen, Rui; Halder, Georg; Ferguson, Laura; Chamberlain, Nicola; ffrench-Constant, Richard; Kapan, Durrell D; Jiggins, Chris D; Reed, Robert D; McMillan, William O

2008-01-01

192

Critical cytoplasmic region of the interleukin 6 signal transducer gp130 is conserved in the cytokine receptor family.  

PubMed Central

Interleukin 6 (IL-6) signal is transduced through gp130 that associates with a complex of IL-6 and IL-6 receptor. Truncations or amino acid substitutions offe introduced in the cytoplasmic region of human gp130, and the mutant cDNAs were transfected into murine interleukin 3-dependent cells to determine amino acid residues critical for generating the IL-6-mediated growth signal. In the 277-amino acid cytoplasmic region of gp130, a 61-amino acid region proximal to the transmembrane domain was sufficient for generating the growth signal. In this region, two short segments were significantly homologous with other cytokine-receptor family members. One segment is conserved in almost all members of the family, and the other is found especially in granulocyte colony-stimulating factor receptor, interleukin 2 receptor beta chain, erythropoietin receptor, KH97 (a granulocyte/macrophage colony-stimulating factor receptor-associated molecule), and interleukin 3 receptor. gp130 molecules with mutations in either of these two segments could not transduce growth signal. Loss of signal-transducing ability of gp130 with such a mutation coincided with disappearance of IL-6-induced tyrosine phosphorylation of gp130. Images

Murakami, M; Narazaki, M; Hibi, M; Yawata, H; Yasukawa, K; Hamaguchi, M; Taga, T; Kishimoto, T

1991-01-01

193

A conserved central region of yeast Ada2 regulates the histone acetyltransferase activity of Gcn5 and interacts with phospholipids.  

PubMed

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex of Saccharomyces cerevisiae contains more than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5, preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. Sequence alignments of Ada2 homologs indicate a conserved approximately 120-amino-acid-residue central region. To examine the function of this region, we constructed ada2 alleles with mutations of clustered conserved residues. One of these alleles, ada2-RLR (R211S, L212A, and R215A), resulted in an approximately threefold reduction in transcriptional activation of the PHO5 gene and growth changes that parallel deletion of ada2. Microarray analyses further revealed that ada2-RLR alters expression of a subset of those genes affected by deletion of ada2. Indicative of Ada2-RLR affecting Gcn5 function, Ada2-RLR resulted in a decrease in Gcn5-mediated histone acetylation in vitro to a level approximately 40% that with wild-type Ada2. In addition, in vivo acetylation of K16 of histone H2B was almost totally eliminated at Ada2-regulated promoters in the ada2-RLR strain, while acetylation of K9 and K18 of histone H3 was reduced to approximately 40% of wild-type levels. We also show that the central region of Ada2 interacts with phospholipids. Since phosphatidylserine binding paralleled Ada2 function, we suggest that lipid binding may play a role in the function or regulation of the SAGA complex. PMID:18950642

Hoke, Stephen M T; Genereaux, Julie; Liang, Gaoyang; Brandl, Christopher J

2008-10-11

194

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

195

Conserved Linkage within a 4-Cm Region of Mouse Chromosome 9 and Human Chromosome 11  

PubMed Central

A six-point cross was carried out to determine the gene order and distances among loci on mouse chromosome 9. Our results are consistent with the following arrangement: centromere – Lap-1 – (1.2 ± 0.8) – Es-17 – (3.0 ± 1.0) – Ups – (1.3 ± 0.7) – Alp-1 – (23.1 ± 3.4) – Mod-1 – (10.9 ± 2.6) – Acy-1 . This study provides the first estimate of the distances between Es-17, Ups and Alp-1. Exceptions to the preferred association of alleles of Es-17 and Ups have been found in three feral populations and one inbred strain. Evidence is presented for the homology of this chromosome region with the ESA4 – UPS – APO-AI region on the long arm of human chromosome 11.

Antonucci, T. K.; Von Deimling, O. H.; Rosenblum, B. B.; Skow, L. C.; Meisler, M. H.

1984-01-01

196

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

197

Bryozoan biodiversity in the New Zealand region and implications for marine conservation  

Microsoft Academic Search

Marine biodiversity and its distribution in the New Zealand region were determined using historical data for an appropriate indicator taxon, the Bryozoa. Bryozoans were identified as belonging to three communities, termed Intertidal\\/Shelf\\/Slope (ISS) and Deep-Sea 1 and 2 (DS1 and DS2). Biodiversity was assessed using measures based on relatedness of species, average taxonomic distinctness and variation in taxonomic distinctness. High

A. A. Rowden; R. M. Warwick; D. P. Gordon

2004-01-01

198

Characterization of conservative somatic instability of the CAG repeat region in Huntington`s disease  

Microsoft Academic Search

Instability and enlargement of a CAG repeat region at the beginning of the huntingtin gene (IT-15) has been linked with Huntington`s disease. The CAG repeat size shows a highly significant correlation with age-of-onset of clinicial features in individuals with 40 or more repeats who have Huntington disease. The clinical status of nonsymptomatic individuals with 30 to 39 CAG repeats is

F. V. Schaefer; A. S. Calikoglu; L. H. Whetsell

1994-01-01

199

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

200

Pupils' problems in understanding conservation of matter  

Microsoft Academic Search

This paper describes the acquisition of conservation of matter by students aged 9?15. Students were tested for their ability to recognize weight conservation as well as reversibility of process in the following changes in matter: translocation, melting, dissolving and evaporation. It was found that children who recognized weight conservation in the translocation task did not necessarily recognize the same in

Ruth Stavy

1990-01-01

201

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

202

The role of a conserved region of the second intracellular loop in AT1 angiotensin receptor activation and signaling.  

PubMed

The pleiotropic actions of angiotensin II are mediated by the primarily G(q) protein-coupled type 1 angiotensin (AT(1)) receptor. In this study a mutational analysis of the function of the conserved DRYXXV/IXXPL domain in the second intracellular loop of the rat AT(1A) receptor was performed in COS7 cells. Alanine substitution studies showed that single replacement of the highly conserved Asp(125) and Arg(126), but not Tyr(127), moderately impaired angiotensin II-induced inositol phosphate signaling. However, concomitant substitution of both Asp(125) and Arg(126) caused marked reduction of both inositol phosphate signaling and receptor internalization. Alanine scanning of the adjacent residues showed that substitution of Ile(130), His(132), and Pro(133) reduced agonist-induced inositol phosphate signal generation, whereas mutations of Met(134) also impaired receptor internalization. Expression of the D125A mutant AT(1A) receptor in COS7 cells endowed the receptor with moderate constitutive activity, as indicated by its enhanced basal Elk1 promoter activity and inositol phosphate response to partial agonists. Angiotensin II-induced stimulation of the Elk1 promoter showed parallel impairment with inositol phosphate signal generation in receptors containing mutations in this region of the AT(1A) receptor. These data confirm that Ca(2+) signal generation is required for the nuclear effects of angiotensin II-induced ERK activation. They are also consistent with the role of the conserved DRY sequence of the AT(1A) receptor in receptor activation, and of Asp(125) in constraining the receptor in its inactive conformation. Furthermore, in the cytoplasmic helical extension of the third helix, an apolar surface that includes Ile(130) and Met(134) appears to have a direct role in G protein coupling. PMID:12746278

Gáborik, Zsuzsanna; Jagadeesh, Gowraganahalli; Zhang, Meng; Spät, András; Catt, Kevin J; Hunyady, László

2003-06-01

203

Highly conserved antigenic epitope regions of hemagglutinin and neuraminidase genes between 2009 H1N1 and seasonal H1N1 influenza: vaccine considerations.  

PubMed

An immunoinformatics study was conducted to determine the highly conserved antigenic epitope regions of hemagglutinin (HA) and neuraminidase (NA) genes in the humoral immunity and CD4+ and CD8+ T cellular immunity between 2009 pandemic H1N1 (pH1N1) and seasonal H1N1 (sH1N1) viruses. It was found that in sH1N1 viruses, 29 epitope regions of HA genes and 8 epitope regions of NA genes which had been experimentally identified, were highly conserved (97.1-100.0%) in the corresponding genes and predictive epitopes of the pH1N1 viruses. The results suggested that highly conserved antigenic epitope regions might act as the basis of common antigenic vaccines against pH1N1 and sH1N1 viruses. PMID:23433453

Huang, Ping; Yu, Shouyi; Wu, Changyou; Liang, Lijun

2013-02-22

204

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

205

The sequence organization of Yp/proximal Xq homologous regions of the human sex chromosomes is highly conserved  

SciTech Connect

Detailed deletion analysis of patients with breakpoints in Yp has allowed the definition of two distinct intervals on the Y chromosome short arm outside the pseudoautosomal region that are homologous to Xq21.3. Detailed YAC contigs have been developed over these regions on both the X and Y chromosomes, and the relative order of markers has been compared to assess whether rearrangements on either sex chromosome have occurred since the transposition events creating these patterns of homology. On the X chromosome, the region forms almost one contiguous block of homology, whereas on the Y chromosome, there has been one major rearrangement leading to the two separate Yp-Xq21 blocks of homology. The rearrangement breakpoint has been mapped. Within these separate X-Y homologous blocks on Yp, the order of loci homologous to X has been conserved to a high degree between the sex chromosomes. With the exception of the amelogenin gene (proximal Yp block), all the X-Y homologous sequences in the two Yp blocks have homologues in Xq21.3, with the former having its X counterpart in Xp22.2. This suggests an independent evolutionary event leading to the formation of the amelogenin X-Y homology. 45 refs., 4 figs., 1 tab.

Sargent, C.A.; Briggs, H.; Chalmers, I.J. [Univ. of Cambridge (United Kingdom)] [and others

1996-03-01

206

cDNA sequence, genomic organization, and evolutionary conservation of a novel gene from the WAGR region  

SciTech Connect

A new gene (239FB) with predominant and differential expression in fetal brain has recently been isolated from a chromosome 11p13-p14 boundary area near FSHB. The corresponding mRNA has an open reading frame of 294 amino acids, a 3` untranslated region of 1247 nucleotides, and a highly GC-rich 5` untranslated region. The coding and 3` UT sequence is specified by 6 exons within nearly 87 kb of isolated genomic locus. The 5` end region of the transcript maps adjacent to the only genomically defined CpG island in a chromosomal subregion that may be associated with part of the mental retardation of some WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome patients. In addition to nucleotide and amino acid similarity to an EST from a normalized infant brain cDNA library, the predicted protein has extensive similarity to Caenorhbditis elegans polypeptides of, as yet, unknown function. The 239FB locus is, therefore, likely part of a family of genes with two members expressed in human brain. The extensive conservation of the predicted protein suggests a fundamental function of the gene product and will enable evaluation of the role of the 239FB gene in neurogenesis in model organisms. 48 refs., 4 figs., 1 tab.

Schwartz, F.; Eisenman, R.; Knoll, J.; Bruns, G. [Children`s Hospital and Department of Pediatrics, Boston, MA (United States)

1995-09-20

207

Highly Conserved Non-Coding Sequences and the 18q Critical Region for Short Stature: A Common Mechanism of Disease?  

PubMed Central

Background Isolated growth hormone deficiency (IGHD) and multiple pituitary hormone deficiency (MPHD) are heterogeneous disorders with several different etiologies and they are responsible for most cases of short stature. Mutations in different genes have been identified but still many patients did not present mutations in any of the known genes. Chromosomal rearrangements may also be involved in short stature and, among others, deletions of 18q23 defined a critical region for the disorder. No gene was yet identified. Methodology/Principal Findings We now report a balanced translocation X;18 in a patient presenting a breakpoint in 18q23 that was surprisingly mapped about 500 Kb distal from the short stature critical region. It separated from the flanking SALL3 gene a region enriched in highly conserved non-coding elements (HCNE) that appeared to be regulatory sequences, active as enhancers or silencers during embryonic development. Conclusion We propose that, during pituitary development, the 18q rearrangement may alter expression of 18q genes or of X chromosome genes that are translocated next to the HCNEs. Alteration of expression of developmentally regulated genes by translocation of HCNEs may represent a common mechanism for disorders associated to isolated chromosomal rearrangements.

Rizzolio, Flavio; Bione, Silvia; Sala, Cinzia; Tribioli, Carla; Ciccone, Roberto; Zuffardi, Orsetta; di Iorgi, Natascia; Maghnie, Mohamad; Toniolo, Daniela

2008-01-01

208

An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region.  

PubMed

Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab. PMID:22419837

Sahu, Mousumi; Sahu, Jagajjit; Sahoo, Smita; Dehury, Budheswar; Sarma, Kishore; Sarmah, Ranjan; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

2012-02-28

209

Site-specific mutagenesis of a highly conserved region of the herpes simplex virus type 1 DNA polymerase gene.  

PubMed Central

Seven point mutations were introduced into region I of the herpes simplex virus type 1 DNA polymerase, which is most highly conserved among DNA polymerases and has no drug sensitivity markers mapped to it. The functional consequences of these mutations were studied in an in vitro transcription-translation system in which T7 transcripts of cloned polymerase genes were used to generate enzymatically active polypeptides in reticulocyte lysate. Analysis of labeled polypeptides on sodium dodecyl sulfate-polyacrylamide gel electrophoresis failed to show any alterations of stability caused by these mutations. The mutations G885R, D886N, T887K, D888A, and G896V lacked polymerase activity and failed to be stimulated by cotranslation of the herpes simplex virus 65-kilodalton DNA-binding protein, whereas R881G and S889A retained both polymerase activity and the capacity to be stimulated by the 65-kilodalton DNA-binding protein. Images

Dorsky, D I; Crumpacker, C S

1990-01-01

210

Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.  

PubMed Central

Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in their function or tissue specificity. A similar pattern of sequence conservation in the 3' UTR is also found in several other genes. Furthermore, while there is a great variation in the size of the 3' UTR of mRNAs coding for different proteins, mRNA coding for isotypic proteins in distantly related organisms often have 3' UTR of similar size. The data suggest that the 3' UTR may play an important role in the regulation of expression of at least some genes at the transcriptional or posttranscriptional level.

Yaffe, D; Nudel, U; Mayer, Y; Neuman, S

1985-01-01

211

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

212

Evolutionary conservation of mechanisms for neural regionalization, proliferation and interconnection in brain development  

PubMed Central

Comparative studies of brain development in vertebrate and invertebrate model systems demonstrate remarkable similarities in expression and action of developmental control genes during embryonic patterning, neural proliferation and circuit formation in the brain. Thus, comparable sets of developmental control genes are involved in specifying the early brain primordium as well as in regionalized patterning along its anteroposterior and dorsoventral axes. Furthermore, similar cellular and molecular mechanisms underlie the formation and proliferation of neural stem cell-like progenitors that generate the neurons in the central nervous systems. Finally, neural identity and some complex circuit interconnections in specific brain domains appear to be comparable in vertebrates and invertebrates and may depend on similar developmental control genes.

Reichert, Heinrich

2008-01-01

213

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

214

Quantifying landscape linkages among giant panda subpopulations in regional scale conservation.  

PubMed

Understanding habitat requirements and identifying landscape linkages are essential for the survival of isolated populations of endangered species. Currently, some of the giant panda populations are isolated, which threatens their long-term survival, particularly in the Xiaoxiangling mountains. In the present study, we quantified niche requirements and then identified potential linkages of giant panda subpopulations in the most isolated region, using ecological niche factor analysis and a least-cost path model. Giant pandas preferred habitat with conifer forest and gentle slopes (>20 to ?30°). Based on spatial distribution of suitable habitat, linkages were identified for the Yele subpopulation to 4 other subpopulations (Liziping, Matou, Xinmin and Wanba). Their lengths ranged from 15 to 54 km. The accumulated cost ranged from 693 to 3166 and conifer forest covered over 31%. However, a variety of features (e.g. major roads, human settlements and large unforested areas) might act as barriers along the linkages for giant panda dispersal. Our analysis quantified giant panda subpopulation connectivity to ensure long-term survival. PMID:22691200

Qi, Dunwu; Hu, Yibo; Gu, Xiaodong; Yang, Xuyi; Yang, Guang; Wei, Fuwen

2012-06-01

215

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

216

A Successful Water Conservation Program in a Semiarid Region of Nebraska  

NASA Astrophysics Data System (ADS)

Ground water irrigation pumpage of the High Plains Aquifer is controlled at the state level in Texas and Oklahoma but at the regional level in Kansas and Nebraska. Critical declines in the aquifer that threatened the reliability of local public water supply wells prompted Nebraska's Upper Republican Natural Resources District (URNRD) to mandate water restrictions in 1978. Under current regulations, irrigators may not extract more than 1,842 millimeters of water per certified hectare (ha) in any fiveyear period. Meter monitoring ensures that irrigators comply with restrictions. Farmers now incorporate irrigation scheduling into their cropping practices in order to meet URNRD controls. This study examines whether irrigators are using ground water efficiently while complying with pumpage limits. Crop irrigation requirements (CIR) from 1986 to 1999 were derived from a water balance approach incorporating Penman-Monteith evapotranspiration (ET) calculations from weather data supplied by the High Plains Climate Center automated weather station network. A ratio of average water pumped per well to the CIR was developed to verify irrigation efficiency. Results indicate that irrigation applications were less than CIR during most irrigation seasons. Irrigation efficiency increases can be attributed to crop rotations, favorable growing season precipitation, use of ET estimates to schedule irrigation, and water allocations limited to less than all certified hectares.

Adelman, Donald D.

2003-10-01

217

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

218

Characterization of conservative somatic instability of the CAG repeat region in Huntington`s disease  

SciTech Connect

Instability and enlargement of a CAG repeat region at the beginning of the huntingtin gene (IT-15) has been linked with Huntington`s disease. The CAG repeat size shows a highly significant correlation with age-of-onset of clinicial features in individuals with 40 or more repeats who have Huntington disease. The clinical status of nonsymptomatic individuals with 30 to 39 CAG repeats is considered ambiguous. In order to define more carefully the nature of the HD expansion instability, we examined patients in our HD population using a discriminating fluorescence-based PCR approach. The degree of somatic mutation increases with both earlier age of onset and the size of the inherited allele. A single prominent band one repeat larger than the index peak was typical in individuals with 40-41 CAG repeats. Three to four larger bands are typically discerned in individuals with 50 or more repeats. In an extreme example, an individual with approximately 95 repeats had at least 8 prominent bands. Plotting the degree of somatic mutation relative to the size of the HD allele shows somatic mutation activity increases with size. By this approach 40-60% of the alleles in a 40-41 CAG repeat HD loci is represented in the primary allele. In contrast, the primary allele represents a relatively minor proportion of the total alleles for expansions greater than 50 CAG repeats (10-20%). The limited range of somatic mutation suggest that the instability is restricted to very early stages of embryogenesis before tissue development diverges or that persistent somatic instability occurs at a slow rate. Therefore, the properties of somatic instability in Huntington`s disease have aspects that are both in common but also different from that found in other trinucleotide repeat expanding diseases such as myotonic muscular dystrophy and fragile X syndrome.

Schaefer, F.V.; Calikoglu, A.S.; Whetsell, L.H. [H.A. Chapman Research Institute of Medical Genetics, Tulsa, OK (United States)

1994-09-01

219

Two conserved regions within the tissue-type plasminogen activator gene promoter mediate regulation by brain-derived neurotrophic factor.  

PubMed

Tissue-type plasminogen activator (t-PA) has recently been identified as a modulator of neuronal plasticity and can initiate conversion of the pro-form of brain-derived neurotrophic factor (BDNF) into its mature form. BDNF also increases t-PA gene expression implicating t-PA as a downstream effector of BDNF function. Here we demonstrate that BDNF-mediated induction of t-PA mRNA requires an increase in t-PA gene transcription. Reporter constructs harboring 9.5 kb of the human t-PA promoter conferred BDNF-responsiveness in transfected mouse primary cortical neurons. This regulation was recapitulated in HEK 293 cells coexpressing the TrkB neurotrophin receptor. t-PA promoter-deletion analysis revealed the presence of two BDNF-responsive domains, one located between -3.07 and -2.5 kb and the other within the proximal promoter. The upstream region was shown to confer BDNF responsiveness in a TrkB-dependent manner when attached to a heterologous promoter. We also identify homologous regions within the murine and bovine t-PA gene promoters and demonstrate that the equivalent upstream murine sequence functions as a BDNF-responsive enhancer when inserted 5' of the human proximal t-PA promoter. Hence, BDNF-mediated induction of t-PA transcription relies on conserved modular promoter elements including a novel upstream BDNF-responsive domain and the proximal t-PA gene promoter. PMID:17419735

Daniel, Philip B; Lux, Wolfram; Samson, Andre L; Schleuning, Wolf-Dieter; Niego, Be'eri; Weiss, Thomas W; Tjärnlund-Wolf, Anna; Medcalf, Robert L

2007-04-05

220

Conserved region at the COOH terminus of human immunodeficiency virus gp120 envelope protein contains an immunodominant epitope  

SciTech Connect

A highly immunogenic epitope from a conserved COOH-terminal region of the human immunodeficiency virus (HIV) gp120 envelope protein has been identified with antisera from HIV-seropositive subjects and a synthetic peptide (SP-22) containing 15 amino acids from this region (Ala-Pro-Thr-Lys-Ala-Lys-Arg-Arg-Val-Val-Gln-Arg-Glu-Lys-Arg). Peptide SP-22 absorbed up to 100% of anti-gp120 antibody reactivity from select HIV/sup +/ patient sera in immunoblot assays and up to 79% of serum anti-gp120 antibody reactivity in competition RIA. In RIA, 45% of HIV-seropositive subjects had antibodies that bound to peptide SP-22. Human anti-SP-22 antibodies that bound to and were eluted from an SP-22 affinity column reacted with gp120 in RIA and immunoblot assays but did not neutralize HIV or inhibit HIV-induced syncytium formation in vitro, even though these antibodies comprised 70% of all anti-gp120 antibodies in the test serum. In contrast, the remaining 30% of SP-22 nonreactive anti-gp120 antibodies did not react with gp120 in immunoblot assays but did react in RIA and neutralized HIV in vitro. Thus, approx. = 50% of HIV-seropositive patients make high titers of nonneutralizing antibodies to an immunodominant antigen on gp120 defined by SP-22. Moreover, the COOH terminus of gp120 contains the major antigen or antigens identified by human anti-gp120 antibodies in immunoblot assays.

Palker, T.J.; Matthews, T.J.; Clark, M.E.; Cianciolo, G.J.; Randall, R.R.; Langlois, A.J.; White, G.C.; Safai, B.; Snyderman, R.; Bolognesi, D.P.; Haynes, B.F.

1987-04-01

221

Balanced translocation in a patient with craniosynostosis disrupts the SOX6 gene and an evolutionarily conserved non-transcribed region.  

PubMed

Craniosynostosis is a congenital developmental disorder involving premature fusion of cranial sutures, which results in an abnormal shape of the skull. Significant progress in understanding the molecular basis of this phenotype has been made for a small number of syndromic craniosynostosis forms. Nevertheless, in the majority of the approximately 100 craniosynostosis syndromes and in non-syndromic craniosynostosis the underlying gene defects and pathomechanisms are unknown. Here we report on a male infant presenting at birth with brachycephaly, proptosis, midfacial hypoplasia, and low set ears. Three dimensional cranial computer tomography showed fusion of the lambdoid sutures and distal part of the sagittal suture with a gaping anterior fontanelle. Mutations in the genes for FGFR2 and FGFR3 were excluded. Standard chromosome analysis revealed a de novo balanced translocation t(9;11)(q33;p15). The breakpoint on chromosome 11p15 disrupts the SOX6 gene, known to be involved in skeletal growth and differentiation processes. SOX6 mutation screening of another 104 craniosynostosis patients revealed one missense mutation leading to the exchange of a highly conserved amino acid (p.D68N) in a single patient and his reportedly healthy mother. The breakpoint on chromosome 9 is located in a region without any known or predicted genes but, interestingly, disrupts patches of evolutionarily highly conserved non-genic sequences and may thus led to dysregulation of flanking genes on chromosome 9 or 11 involved in skull vault development. The present case is one of the very rare reports of an apparently balanced translocation in a patient with syndromic craniosynostosis, and reveals novel candidate genes for craniosynostoses and cranial suture formation. PMID:16258006

Tagariello, A; Heller, R; Greven, A; Kalscheuer, V M; Molter, T; Rauch, A; Kress, W; Winterpacht, A

2005-10-28

222

Regional nodal recurrence in breast cancer patients treated with conservative surgery and radiation therapy (BCS+RT)  

SciTech Connect

Purpose: To review regional nodal (RN) management and identify predictors of RN relapse in patients treated with breast conserving surgery and radiation therapy (BCS+RT). Methods and Materials: Patients with Stage I and II breast cancer (N = 1920) underwent BCS+RT from 1973 to 2003. Patients undergoing RN were treated with a median dose of 46 Gy. Patients undergoing axillary dissection (AXD, N = 1330) were treated to the breast alone if node-negative (N = 984), and to the breast and supraclavicular fossa if node-positive (N = 346). Patients who did not undergo AXD (N = 590) were treated with RT to the supraclavicular fossa and axilla. Sentinel node biopsy (SNB) was performed on 126 patients. SN-negative patients (N = 110) were treated with tangents only. There were 16 SN-positive patients who did not undergo complete AXD and were treated with RT. Results: As of September 2005, there have been 36 RN relapses for an actuarial nodal control rate (NCR) of 98% at 10 years. There was no difference in NCR between those undergoing AXD (NCR = 97.4%) and those receiving RT without AXD (NCR = 97.9%). In multivariate analysis, young age, non-Caucasian race, and pathologic nodal status correlated with increased risk of nodal relapse. Of the 126 patients undergoing SNB, there was only 1 nodal recurrence. None of the 16 SN-positive patients treated with RT without AXD had nodal failure. Conclusions: In patients undergoing BCS+RT, both regional nodal irradiation and AXD (including SNB) resulted in equally high rates of regional nodal control. Nodal RT may also be an effective treatment for SN-positive patients.

Pejavar, Sunanda [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States); Wilson, Lynn D. [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT (United States); Haffty, Bruce G. [Department of Radiation Oncology, UMDNJ-Robert Wood Johnson Medical School and Cancer Institute of New Jersey, New Brunswick, NJ (United States)]. E-mail: hafftybg@umdnj.edu

2006-12-01

223

Autoantibody germ-line gene segment encodes V{sub H} and V{sub L} regions of a human anti-streptococcal monoclonal antibody recognizing streptococcal M protein and human cardiac myosin epitopes  

SciTech Connect

Cross-reactivity of anti-streptococcal Abs with human cardiac myosin may result in sequelae following group A streptococcal infections. Molecular mimicry between group A streptococcal M protein and cardiac myosin may be the basis for the immunologic cross-reactivity. In this study, a cross-reactive human anti-streptococcal/antimyosin mAb (10.2.3) was characterized, and the myosin epitopes were recognized by the Ab identified. mAb 10.2.3 reacted with four peptides from the light meromyosin (LMM) tail fragment of human cardiac myosin, including LMM-10 (1411-1428), LMM-23 (1580-1597), LMM-27 (1632-1649), and LMM-30 (1671-1687). Only LMM-30 inhibited binding of mAb 10.2.3 to streptococcal M protein and human cardiac myosin. Human mAb 10.2.3 labeled cytoskeletal structures within rat heart cells in indirect immunofluorescence, and reacted with group A streptococci expressing various M protein serotypes, PepM5, and recombinant M protein. The nucleotide sequence of gene segments encoding the Ig heavy and light chain V region of mAb 10.2.3 was determined. The light chain V segment was encoded by a VK1 gene segment that was 98.5% identical with germ-line gene humig{sub K}Vi5. The V segment of the heavy chain was encoded by a V{sub H}3a gene segment that differed from the V{sub H}26 germ-line gene by a single base change. V{sub H}26 is expressed preferentially in early development and encodes autoantibodies with anti-DNA and rheumatoid factor specificities. Anti-streptococcal mAb 10.2.3 is an autoantibody encoded by V{sub H} and V{sub L} genes, with little or no somatic mutation. 63 refs., 11 figs.

Quinn, A.; Cunningham, M.W. [Univ. of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Adderson, E.E. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

1995-04-15

224

The chick and human collagen alpha1(XII) gene promoter--activity of highly conserved regions around the first exon and in the first intron.  

PubMed

A single gene encodes collagen XII, an extracellular matrix protein with three large fibronectin-related subunits connected via a short collagen triple helix. Since collagen XII is a component of a specific subset of collagen fibrils in tissues bearing high tensile stress, we are interested to know how its restricted expression is regulated. To this aim, we have isolated the region around the first exon of both the chick and human collagen alpha1(XII) gene. The upstream sequences of the two genes share common features but are not related. Strong similarity starts about 100 bp 5' of the first exon and ends 100 bp into the first intron. In addition, two large conserved regions (56-63% similarity) were found in the first intron. A single major and two clusters of minor transcription start sites were identified in both the chick and human gene. To test for promoter activity, conserved fragments from the chick gene were cloned into reporter plasmids for transient transfection of fibroblasts. A 70-bp stretch containing a conserved nuclear factor-1 binding sequence just upstream of the first transcription start site was found to work as a basal promoter. An adjacent, but nonoverlapping short segment including the more downstream start sites and a conserved TATTAA sequence exhibited independent promoter activity. GC-rich sequences just 5' and 3' of the minimal promoter fragments were required for full activity. In contrast, inclusion of more upstream sequences (up to 2.4 kb) had no effect. The two conserved regions in the first intron showed no promoter activity on their own but modulated activity when linked to autologous or heterologous promoters. Specifically, one of these intronic regions might contain enhancer element(s) that respond to mechanical stress acting on the fibroblasts. We conclude that the collagen XII gene is driven by a basal promoter with two halves that can act independently; conserved control regions are located around the first exon and in the first intron. PMID:9826181

Chiquet, M; Mumenthaler, U; Wittwer, M; Jin, W; Koch, M

1998-10-15

225

The fully conserved Asp residue in conserved sequence region I of the alpha-amylase family is crucial for the catalytic site architecture and activity.  

PubMed

The alpha-amylase family is a large group of starch processing enzymes [Svensson, B. (1994) Plant Mol. Biol. 25, 141-157]. It is characterized by four short sequence motifs that contain the seven fully conserved amino acid residues in this family: two catalytic carboxylic acid residues and four substrate binding residues. The seventh conserved residue (Asp135) has no direct interactions with either substrates or products, but it is hydrogen-bonded to Arg227, which does bind the substrate in the catalytic site. Using cyclodextrin glycosyltransferase as an example, this paper provides for the first time definite biochemical and structural evidence that Asp135 is required for the proper conformation of several catalytic site residues and therefore for activity. PMID:12706817

Leemhuis, Hans; Rozeboom, Henriëtte J; Dijkstra, Bauke W; Dijkhuizen, Lubbert

2003-04-24

226

Ecology of the entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae in temperate agroecosystems: Potential for conservation biological control  

Microsoft Academic Search

It is increasingly recognized that the biodiversity in agroecosystems deliver significant ecosystem services to agricultural production such as biological control of pests. Entomopathogenic fungi, specifically the anamorphic taxa Beauveria bassiana and Metarhizium anisopliae, Hypocreales (Ascomycota), are among the natural enemies of pests in agroecosystems and the fungi are candidates for future conservation biological control in temperate regions. Conservation biological control

Nicolai V. Meyling; Jřrgen Eilenberg

2007-01-01

227

Nuclear Matrix Attachment Regions of Human Papillomavirus Type 16 Point toward Conservation of These Genomic Elements in All Genital Papillomaviruses  

PubMed Central

The gene functions, transcriptional regulation, and genome replication of human papillomaviruses (HPVs) have been extensively studied. Thus far, however, there has been little research on the organization of HPV genomes in the nuclei of infected cells. As a first step to understand how chromatin and suprachromatin structures may modulate the life cycles of these viruses, we have identified and mapped interactions of HPV DNAs with the nuclear matrix. The endogenous genomes of HPV type 16 (HPV-16) which are present in SiHa, HPKI, and HPKII cells, adhere in vivo to the nuclear matrixes of these cell lines. A tight association with the nuclear matrix in vivo may be common to all genital HPV types, as the genomes of HPV-11, HPV-16, HPV-18, and HPV-33 showed high affinity in vitro to preparations of the nuclear matrix of C33A cells, as did the well-known nuclear matrix attachment region (MAR) of the cellular beta interferon gene. Affinity to the nuclear matrix is not evenly spread over the HPV-16 genome. Five genomic segments have strong MAR properties, while the other parts of the genome have low or no affinity. Some of the five MARs correlate with known cis-responsive elements: a strong MAR lies in the 5? segment of the long control region (LCR), and another one lies in the E6 gene, flanking the HPV enhancer, the replication origin, and the E6 promoter. The strongest MAR coincides with the E5 gene and the early-late intergenic region. Weak MAR activity is present in the E1 and E2 genes and in the 3? part of L2. The in vitro map of MAR activity appears to reflect MAR properties in vivo, as we found for two selected fragments with and without MAR activity. As is typical for many MARs, the two segments with highest affinity, namely, the 5? LCR and the early-late intergenic region, have an extraordinarily high A-T content (up to 85%). It is likely that these MARs have specific functions in the viral life cycle, as MARs predicted by nucleotide sequence analysis, patterns of A-T content, transcription factor YY1 binding sites, and likely topoisomerase II cleavage sites are conserved in similar positions throughout all genital HPVs.

Tan, Shyh-Han; Bartsch, Dusan; Schwarz, Elisabeth; Bernard, Hans-Ulrich

1998-01-01

228

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

229

An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach  

Microsoft Academic Search

In previous work, we presented GAMI [1], an approach to motif inference that uses a genetic algorithms search. GAMI is designed specifically to find putative conserved regulatory motifs in noncoding regions of divergent species, and is designed to allow for analysis of long nucleotide sequences. In this work, we compare GAMI's performance when run with its original fitness function (a

Clare Bates Congdon; Joseph C. Aman; Gerardo M. Nava; H. Rex Gaskins; Carolyn J. Mattingly

2008-01-01

230

Induction of autoimmune valvulitis in Lewis rats following immunization with peptides from the conserved region of group A streptococcal M protein  

Microsoft Academic Search

Rheumatic heart disease (RHD) is considered to be an autoimmune disorder mediated by group A streptococcal (GAS) M protein-specific T cells and antibodies that cross-react with cardiac antigens and epitopes of the GAS M protein. In this study, Lewis rats were immunized with a pool of overlapping peptides spanning the conserved region of the GAS M protein in Complete Freund's

Robyn S. Lymbury; Colleen Olive; Kellie A. Powell; Michael F. Good; Robert G. Hirst; Justin T. LaBrooy; Natkunam Ketheesan

2003-01-01

231

The potential for electricity generation from on-shore wind energy under the constraints of nature conservation: a case study for two regions in Germany  

Microsoft Academic Search

In spite of the well-acknowledged environmental benefits of electricity generation from wind energy, there is increasing concern about impacts from wind turbines on local ecosystems and on the natural scenery. A GIS-based approach is developed to analyse the effect of different nature conservation criteria on the wind energy potential in quantitative terms. Results for two case study regions in Germany,

W. Krewitt; J. Nitsch

2003-01-01

232

Conserving biological diversity: A strategy for protected areas in the Asia-Pacific region. World Bank technical paper  

SciTech Connect

The paper acknowledges the importance of biodiversity conservation and suggests that policy change coupled with the establishment of protected area systems will be critical to success. A wide range of interventions will be needed to support these efforts toward conserving biodiversity-interventions involving national and local governments, national and international nongovernmental organizations and, most importantly, local people. The strategy defined in the paper is intended to complement existing national and international initiatives and to build partnerships in conservation for the 1990s.

Braatz, S.; Davis, G.; Shen, S.; Rees, C.

1992-01-01

233

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

234

The Rhizobium etli ?70 (SigA) factor recognizes a lax consensus promoter  

PubMed Central

A collection of Rhizobium etli promoters was isolated from a genomic DNA library constructed in the promoter-trap vector pBBMCS53, by their ability to drive the expression of a gusA reporter gene. Thirty-seven clones were selected, and their transcriptional start-sites were determined. The upstream sequence of these 37 start-sites, and the sequences of seven previously identified promoters were compared. On the basis of sequence conservation and mutational analysis, a consensus sequence CTTGACN16–23TATNNT was obtained. In this consensus sequence, nine on of twelve bases are identical to the canonical Escherichia coli ?70 promoter, however the R.etli promoters only contain 6.4 conserved bases on average. We show that the R.etli sigma factor SigA recognizes all R.etli promoters studied in this work, and that E.coli RpoD is incapable of recognizing them. The comparison of the predicted structure of SigA with the known structure of RpoD indicated that regions 2.4 and 4.2, responsible for promoter recognition, are different only by a single amino acid, whereas the region 1 of SigA contains 72 extra residues, suggesting that the differences contained in this region could be related to the lax promoter recognition of SigA.

Ramirez-Romero, Miguel A.; Masulis, Irina; Cevallos, Miguel A.; Gonzalez, Victor; Davila, Guillermo

2006-01-01

235

A functional role for the conserved protonatable hairpins in the 5' untranslated region of turnip yellow mosaic virus RNA.  

PubMed

The 5' untranslated region (UTR) of the RNA of several tymoviruses contains conserved hairpins with protonatable internal loops, consisting of C-C and C-A mismatches (K. Hellendoorn, P. J. A. Michiels, R. Buitenhuis, and C. W. A. Pleij, Nucleic Acids Res. 24, 4910-4917, 1996). Here, we present a functional analysis of the 5' UTR of turnip yellow mosaic virus (TYMV) RNA, which contains two protonatable hairpins with nearly identical internal loops. Mutations were introduced in an infectious cDNA clone, and T7 RNA transcripts were used to infect Chinese cabbage plants. Different symptoms were observed for the various mutants, pointing to a functional role of the C-C and C-A mismatches in the hairpins of the 5' UTR. The replication of the virus is influenced by the mutations made, while in vitro translation studies showed that the expression of the two overlapping reading frames of TYMV is not influenced by the secondary structure of the leader. Various mutants were propagated for up to five serial passages of infection, and the sequence of the 5' UTR was determined. This resulted in virus RNA with new non-wild-type sequences that produced the wild-type phenotype in infected plants. Remarkably, in all cases C-C or C-A mismatches were introduced. The internal loop of the 5'-proximal hairpin seems to be more important for the viral life cycle than that of the second hairpin. A deletion of 75% of the leader, including the two hairpins, resulted in a virus that was deficient in viral spread. Since the ratio between filled and empty capsids was changed drastically by this mutation, a role of the 5' UTR in viral packaging is proposed. PMID:9343237

Hellendoorn, K; Verlaan, P W; Pleij, C W

1997-11-01

236

[Analysis of soil respiration and influence factors in wheat farmland under conservation tillage in southwest hilly region].  

PubMed

In order to investigate the effect of conservation tillage on soil respiration in dry cropping farmland in southwest purple hilly region, the LI6400-09 respiratory chamber was adopted in the experiment conducted in the experimental field in Southwest University in Beibei, Chongqing. The respiration and the hydrothermal and biotic factors of soil were measured and analyzed during the growth period of wheat in the triple intercropping system of wheat/maize/soybean. There were four treatments including T (traditional tillage), R (ridge tillage), TS (traditional tillage + straw mulching) and RS (ridge tillage + straw mulching), which were all in triplicates. The results indicated that the soil respiration rate changed in the range of 1.100-2.508 micromol x (m2 x s)(-1) during the reproductive growth stage of wheat. There were significant differences in soil respiration rate among different treatments, which could be ranked as RS > R > TS > T. The soil temperature in the 10cm layer was ranked as T > R > TS > RS. The relationship between soil respiration and soil temperature fitted well with an exponential function, in which the Q10 values were 1.25, 1.20, 1.31 and 1.26, respectively. The soil moisture in the 5cm layer was ranked as TS > RS > T > R. The best fitting model between soil moisture and soil respiration was a parabolic curve, indicating the presence of soil moisture with the strongest soil respiration. The response threshold of wheat to soil moisture was 14.80%-17.47% during the reproductive stage. The dominant groups of soil animals were Collembola and Acarina, which were correlated with soil respiration to some extent. The correlation was high in the treatments T and R, ranged from 0.669-0.921, whereas there was no remarkable correlation in the other treatments. PMID:24028018

Zhang, Sai; Zhang, Xiao-Yu; Wang, Long-Chang; Luo, Hai-Xiu; Zhou, Hang-Fei; Ma, Zhong-Lian; Zhang, Cui-Wei

2013-07-01

237

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

238

Recognizing Action at a Distance  

Microsoft Academic Search

Our goal is to recognize human actions at a distance, at resolutions where a whole person may be, say, 30 pix- els tall. We introduce a novel motion descriptor based on optical flow measurements in a spatio-temporal volume for each stabilized human figure, and an associated similarity measure to be used in a nearest-neighbor framework. Mak- ing use of noisy

Alexei A. Efros; Alexander C. Berg; Greg Mori; Jitendra Malik

2003-01-01

239

A Lipid Core Peptide Construct Containing a Conserved Region Determinant of the Group A Streptococcal M Protein Elicits Heterologous Opsonic Antibodies  

PubMed Central

The study reported here investigated the immunogenicity and protective potential of a lipid core peptide (LCP) construct containing a conserved region determinant of M protein, defined as peptide J8. Parenteral immunization of mice with LCP-J8 led to the induction of high-titer serum immunoglobulin G J8-specific antibodies when the construct was coadministered with complete Freund's adjuvant (CFA) or administered alone. LCP-J8 in CFA had significantly enhanced immunogenicity compared with the monomeric peptide J8 given in CFA. Moreover, LCP-J8/CFA and LCP-J8 antisera opsonized four different group A streptococcal (GAS) strains, and the antisera did not cross-react with human heart tissue proteins. These data indicate the potential of an LCP-based M protein conserved region GAS vaccine in the induction of broadly protective immune responses in the absence of a conventional adjuvant.

Olive, Colleen; Batzloff, Michael R.; Horvath, Aniko; Wong, Allan; Clair, Timothy; Yarwood, Penny; Toth, Istvan; Good, Michael F.

2002-01-01

240

The X chromosome of monotremes shares a highly conserved region with the eutherian and marsupial X chromosomes despite the absence of X chromosome inactivation  

SciTech Connect

Eight genes, located on the long arm of the human X chromosome and present on the marsupial X chromosome, were mapped by in situ hybridization to the chromosomes of the platypus Ornithorhynchus anatinus, one of the three species of monotreme mammals. All were located on the X chromosome. The authors conclude that the long arm of the human X chromosome represents a highly conserved region that formed part of the X chromosome in a mammalian ancestor at least 150 million years ago. Since three of these genes are located on the long arm of the platypus X chromosome, which is G-band homologous to the Y chromosome and apparently exempt from X chromosome inactivation, the conservation of this region has evidently not depended on isolation by X-Y chromosome differentiation and X chromosome inactivation.

Watson, J.M.; Spencer, J.A.; Graves, J.A.M. (La Trobe Univ., Bundoora, Victoria (Australia)); Riggs, A.D. (Beckman Inst., Duarte, CA (USA))

1990-09-01

241

Conserved Sequences in a Tissue-Specific Regulatory Region of the pdx-1 Gene Mediate Transcription in Pancreatic   Cells: Role for Hepatocyte Nuclear Factor 3  and Pax6  

Microsoft Academic Search

Pancreas duodenum homeobox 1 (PDX-1) is absolutely required for pancreas development and the main- tenance of islet -cell function. Temporal and cell-type-specific transcription of the pdx-1 gene is controlled by factors acting upon sequences found within its 5-flanking region. Critical cis-acting transcriptional control elements are located within a nuclease hypersensitive site that contains three conserved subdomains, termed areas I, II,

Susan E. Samaras; Michelle A. Cissell; Kevin Gerrish; Christopher V. E. Wright; Maureen Gannon; Roland Stein

2002-01-01

242

Identification of a hypervariable region containing new Legionella pneumophila Icm/Dot translocated substrates by using the conserved icmQ regulatory signature.  

PubMed

Legionella pneumophila is an intracellular pathogen that has been shown to utilize the Icm/Dot type IV secretion system for pathogenesis. This system was shown to be composed of Icm/Dot complex components, accessory proteins, and a large number of translocated substrates. In this study, comparison of the icmQ regulatory regions from many Legionella species revealed a conserved regulatory sequence that includes the icmQ -10 promoter element. Mutagenesis of this conserved regulatory element indicated that each of the nucleotides in it affects the level of expression of the icmQ gene but not in a uniform fashion. A genomic analysis discovered that four additional genes in L. pneumophila contain this conserved regulatory sequence, which was found to function similarly in these genes as well. Examination of these four genes indicated that they are dispensable for intracellular growth, but two of them were found to encode new Icm/Dot translocated substrates (IDTS). Comparison of the genomic regions encoding these two IDTS among the four available L. pneumophila genomic sequences indicated that one of these genes is located in a hypervariable genomic region, which was shown before to contain an IDTS-encoding gene. Translocation analysis that was performed for nine proteins encoded from this hypervariable genomic region indicated that six of them are new IDTS which are translocated into host cells in an Icm/Dot-dependent manner. Furthermore, a bioinformatic analysis indicated that additional L. pneumophila genomic regions that contain several neighboring IDTS-encoding genes are hypervariable in gene content. PMID:18694969

Zusman, Tal; Degtyar, Elena; Segal, Gil

2008-08-11

243

Activation and repression of glucose-stimulated ChREBP requires the concerted action of multiple domains within the MondoA conserved region  

PubMed Central

Carbohydrate response element-binding protein (ChREBP) is a glucose-dependent transcription factor that stimulates the expression of glycolytic and lipogenic genes in mammals. Glucose regulation of ChREBP has been mapped to its conserved NH2-terminal region of 300 amino acids, designated the MondoA conserved region (MCR). Within the MCR, five domains (MCR1–5) have a particularly high level of conservation and are likely to be important for glucose regulation. We carried out a large-scale deletion and substitution mutational analysis of the MCR domain of ChREBP. This analysis revealed that MCRs 1–4 function in a concerted fashion to repress ChREBP activity in basal (nonstimulatory) conditions. Deletion of the entire MCR1–4 segment or the combination of four specific point mutations located across this region leads to a highly active, glucose-independent form of ChREBP. However, deletion of any individual MCR domain and the majority of point mutations throughout MCR1–4 rendered ChREBP inactive. These observations suggest that the MCR1–4 region interacts with an additional coregulatory factor required for activation. This possibility is supported by the observation that the MCR1–4 region can compete for activity with wild-type ChREBP in stimulatory conditions. In contrast, mutations in the MCR5 domain result in increased activity, suggesting that this domain may be the target of intramolecular repression in basal conditions. Thus, the MCR domains act in a complex and coordinated manner to regulate ChREBP activity in response to glucose.

Davies, Michael N.; O'Callaghan, Brennon L.

2010-01-01

244

Using abiotic data for conservation assessments over extensive regions: quantitative methods applied across New South Wales, Australia  

Microsoft Academic Search

New South Wales (NSW) can be regarded as one of the more “data-rich” parts of the world but its detailed biological data sets, like others elsewhere, are localised. These data are therefore not useable over large geographical areas for consistent reviews of established protected areas or future conservation priorities. In this sense, the constraints of data are similar to those

R. L. Pressey; T. C. Hager; K. M. Ryan; J. Schwarz; S. Wall; S. Ferrier; P. M. Creaser

2000-01-01

245

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

Microsoft Academic Search

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

Chilaka Sabarinadh; Subbaya Subramanian; Rakesh K Mishra

2003-01-01

246

A method of statistical modelling of coral reef fish distribution: Can it aid conservation planning in data poor regions?  

Microsoft Academic Search

Conservation planning for biodiversity requires spatially continuous species data that encompasses the area of interest. Because of the lack of such data in most coral reef settings, we developed a statistical model to expand site-specific coral reef fish species counts to continuous spatial data. Biotic and abiotic reef characteristics were evaluated in their suitability to serve as predictor variables. These

Maria BEGER; Geoffrey P. JONES; Hugh P. POSSINGHAM

2006-01-01

247

The Value of Conservation  

Microsoft Academic Search

As part of growing public debate on sustainability in New Zealand, the Department of Conservation commissioned studies in 2004-2006 on the regional economic impacts of selected activities and ecosystem services on public conservation land. In particular, claims had been made that public conservation land is a \\

Harry Broad; Geoff Butcher; John Waugh; Bernie Napp

2007-01-01

248

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

249

Conserved nucleotides in the terminus of the 3' UTR region are important for the replication and infectivity of porcine reproductive and respiratory syndrome virus.  

PubMed

The 3' untranslated region (3' UTR), including the poly (A) tail, reportedly plays an important role in arterivirus replication, but the roles of the cis-acting elements present in the 3' UTR of porcine reproductive and respiratory syndrome virus (PRRSV) remain largely unknown. In the present study, PCR-based mutagenic analysis was conducted on the 3' UTR of PRRSV infectious full-length cDNA clone pAPRRS to investigate the structure and function of the conserved terminal nucleotides between the poly (A) tail and the 3' UTR region. Our findings indicated that the conservation of the primary sequence of the 3' terminal nucleotides, rather than the surrounding secondary structure, was vital for viral replication and infectivity. Four nucleotides (nt) (5'-(15517)AAUU(15520)-3') at the 3' proximal end of the 3' UTR and the dinucleotide 5'-AU-3' exerted an important regulatory effect on viral viability. Of the five 3'-terminal nucleotides of the 3' UTR (5'-(15503)AACCA(15507)-3'), at least three, including the last dinucleotide (5'-CA-3'), were essential for maintaining viral infectivity. Taken together, the 3'-terminal conserved sequence plays a critical role in PRRSV replication and may function as a contact site for specific assembly of the replication complex. PMID:23512575

Yin, Yang; Liu, Changlong; Liu, Ping; Yao, Huochun; Wei, Zuzhang; Lu, Jiaqi; Tong, Guangzhi; Gao, Fei; Yuan, Shishan

2013-03-13

250

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

251

Comprehensive conservation planning to protect biodiversity and ecosystem services in Canadian boreal regions under a warming climate and increasing exploitation  

Microsoft Academic Search

Boreal regions contain more than half of the carbon in forested regions of the world and over 60% of the world’s surface freshwater. Carbon storage and the flood control and water filtration provided by freshwaters and wetlands have recently been identified as the most important ecosystem services provided by boreal regions, with a value many times greater than current resource

D. W. Schindler; P. G. Lee

2010-01-01

252

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

253

Identification of evolutionarily conserved, functional noncoding elements in the promoter region of the sodium channel gene SCN8A  

Microsoft Academic Search

SCN8A is a major neuronal sodium channel gene expressed throughout the central and peripheral nervous systems. Mutations of SCN8A result in movement disorders and impaired cognition. To investigate the basis for the tissue-specific expression of SCN8A, we located conserved, potentially regulatory sequences in the human, mouse, chicken, and fish genes by 5? RACE of brain\\u000a RNA and genomic sequence comparison.

Valerie L. Drews; Kehui Shi; Georgius de Haan; Miriam H. Meisler

2007-01-01

254

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

Microsoft Academic Search

BackgroundMutations 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

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

2011-01-01

255

Secondary Structures for 5? Regions of R2 Retrotransposon RNAs Reveal a Novel Conserved Pseudoknot and Regions that Evolve under Different Constraints  

Microsoft Academic Search

Sequences from the 5? region of R2 retrotransposons of four species of silk moth are reported. In Bombyx mori, this region of the R2 messenger RNA contains a binding site for R2 protein and mediates interactions critical to R2 element insertion into the host genome. A model of secondary structure for a segment of this RNA is proposed on the

Elzbieta Kierzek; Shawn M. Christensen; Thomas H. Eickbush; Ryszard Kierzek; Douglas H. Turner; Walter N. Moss

2009-01-01

256

Using Surfaces and Object Models to Recognize Partially Obscured Objects  

Microsoft Academic Search

This paper describes an approach to object loca­ tion based on matching model regions to surface image regions. These matches, together with object models, provide hypotheses about the 3D location of the objects containing the recognized surfaces. When a hypothesis is complete, the program describes the matched data and model surface boundaries in terms of the raw model. These descriptions

Robert B. Fisher

1983-01-01

257

Developmental Regulation of Ganglioside Antigens Recognized by the JONES Antibody  

Microsoft Academic Search

The JONES monoclonal antibody has been immunocyto- chemically associated with regions of the developing rat brain where cell and axon migrations are occurring (Mender- Otero et al., 1988, 1988). In the present study the antigens recognized by the JONES antibody were analyzed in a va- riety of brain regions and at developmental ages selected to correspond to the preceding immunocytochemical

Burkhard Schlosshauer; Andrew S. Blum; Rosalia Mendez-Otero; Colin J. Barnstable; Martha Constantine-Paton

1988-01-01

258

Conservation potential of agricultural water conservation subsidies  

Microsoft Academic Search

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

Ray Huffaker

2008-01-01

259

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

260

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

2013-01-23

261

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

262

[Isolation and amplification cDNA of 8H07 gene conservative region of nematode Heterodera schachtii with high relationship to its rape homolog].  

PubMed

Original method of small regulatory si/miRNA isolation from plant cells was elaborated. PCR amplification of fragment cDNA 8H07 nematode Heterodera schachtii gene was carried out. Using Northern-blot method hybridization of plant si/miRNA with cDNA fragment of conservative region 8H07 gene the presence of their high homology is found out. The amplified cDNA fragment of nematode 8H07 gene in future will be used for creation recombinant gene with complementary antisense dsRNA sequence for increasing resistance of rape plants to parasitic nematodes. PMID:23285744

Tsyhankova, V A; Andrusevych, Ia V; Ponomarenko, S P; Halkin, A P; Blium, Ia B

263

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

264

Recognizing Protein Substructure Similarity Using Segmental Threading  

PubMed Central

Summary Protein template identification is essential to protein structure and function predictions. However, conventional whole-chain threading approaches often fail to recognize conserved substructure motifs when the target and templates do not share the same fold. We develop a new approach, SEGMER, for identifying protein substructure similarities by segmental threading. The target sequence is split into segments of 2–4 consecutive or non-consecutive secondary structural elements, which are then threaded through PDB to identify appropriate substructure motifs. SEGMER is tested on 144 non-redundant hard proteins. When combined with whole-chain threading, the TM-score of alignments and accuracy of spatial restraints of SEGMER increase by 16% and 25%, respectively, compared to that by the whole-chain threading methods only. When tested on 12 Free Modeling targets from CASP8, SEGMER increases the TM-score and contact accuracy by 28% and 48%, respectively. This significant improvement should have important impact on protein structure modeling and functional inference.

Wu, Sitao; Zhang, Yang

2010-01-01

265

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

266

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

267

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

268

Structure and Conservation of Tandem Repeats in the Mitochondrial DNA Control Region of the Least Brook Lamprey ( Lampetra aepyptera )  

Microsoft Academic Search

Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still\\u000a remain about their mode of evolution, function, and phylogenetic distribution. We report phylogenetic and geographic patterns\\u000a of variation of control region repeat sequence and number in a nonparasitic lamprey, Lampetra aepyptera. A survey of populations from throughout the species’ range revealed remarkably low repeat

Matthew M. White; Holly R. Martin

2009-01-01

269

Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region  

PubMed Central

Background The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region. Results We compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human), the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human) bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder). The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors. Conclusions The nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The information about the conservation of the palindromic structure and the settling in primates of the polymorphic feature of HS1.2 show the relevance of these structures in the control and modulation of the Ig production through the formation of possible three-dimensional structures.

2011-01-01

270

Highly conserved CDR3 region in circulating CD4+V?5+ T cells may be associated with cytotoxic activity in Chagas disease  

PubMed Central

Human infection with Trypanosoma cruzi leads to Chagas disease, which presents as several different clinical conditions ranging from an asymptomatic form to a severe dilated cardiomyopathy. Several studies have demonstrated that T cells play a critical role in the development of cardiac pathology, as well as in immunoregulation during chronic disease. However, the mechanisms that drive protective or pathogenic T cell response are not known. We have shown that CD4+ T cells from chagasic patients preferentially express T cell receptor (TCR) ?-chain variable region (V?) 5. The aim of this work was to determine whether T cells expressing this particular V? region displayed variable or restricted CDR3 sequences, as an indicator of the nature of the stimulus leading to the activation of these T cells in vivo. Additionally, we aimed to evaluate phenotypic characteristics of these cells that might be associated with pathology. CDR3 junctional region sequencing of V?5·1 expressing CD4+ T cells revealed the occurrence of a highly homologous CDR3 region with conserved TCR J? region usage among patients with cardiac, but not indeterminate, Chagas disease. Moreover, correlation analysis indicated that the frequency of CD4+V?5·1+ cells is associated with granzyme A expression, suggesting that these cells might display cytotoxic function. Together these results provide new insight into T cell recognition of antigens involved in Chagas disease and suggest that these cells may be implicated in the pathogenesis of chagasic cardiomyopathy.

Menezes, C A S; Sullivan, A K; Falta, M T; Mack, D G; Freed, B M; Rocha, M O C; Gollob, K J; Fontenot, A P; Dutra, W O

2012-01-01

271

Highly conserved CDR3 region in circulating CD4(+)V?5(+) T cells may be associated with cytotoxic activity in Chagas disease.  

PubMed

Human infection with Trypanosoma cruzi leads to Chagas disease, which presents as several different clinical conditions ranging from an asymptomatic form to a severe dilated cardiomyopathy. Several studies have demonstrated that T cells play a critical role in the development of cardiac pathology, as well as in immunoregulation during chronic disease. However, the mechanisms that drive protective or pathogenic T cell response are not known. We have shown that CD4(+) T cells from chagasic patients preferentially express T cell receptor (TCR) ?-chain variable region (V?) 5. The aim of this work was to determine whether T cells expressing this particular V? region displayed variable or restricted CDR3 sequences, as an indicator of the nature of the stimulus leading to the activation of these T cells in vivo. Additionally, we aimed to evaluate phenotypic characteristics of these cells that might be associated with pathology. CDR3 junctional region sequencing of V?5·1 expressing CD4(+) T cells revealed the occurrence of a highly homologous CDR3 region with conserved TCR J? region usage among patients with cardiac, but not indeterminate, Chagas disease. Moreover, correlation analysis indicated that the frequency of CD4(+)V?5·1(+) cells is associated with granzyme A expression, suggesting that these cells might display cytotoxic function. Together these results provide new insight into T cell recognition of antigens involved in Chagas disease and suggest that these cells may be implicated in the pathogenesis of chagasic cardiomyopathy. PMID:22774985

Menezes, C A S; Sullivan, A K; Falta, M T; Mack, D G; Freed, B M; Rocha, M O C; Gollob, K J; Fontenot, A P; Dutra, W O

2012-08-01

272

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea.  

PubMed

BACKGROUND: The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. RESULTS: Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. CONCLUSIONS: Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage. PMID:23586706

Navabi, Zahra-Katy; Huebert, Terry; Sharpe, Andrew G; O Neill, Carmel M; Bancroft, Ian; Parkin, Isobel Ap

2013-04-15

273

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea  

PubMed Central

Background The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. Results Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. Conclusions Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage.

2013-01-01

274

Producing and Recognizing Analogical Relations  

PubMed Central

Analogical reasoning is an important component of intelligent behavior, and a key test of any approach to human language and cognition. Only a limited amount of empirical work has been conducted from a behavior analytic point of view, most of that within Relational Frame Theory (RFT), which views analogy as a matter of deriving relations among relations. The present series of four studies expands previous work by exploring the applicability of this model of analogy to topography-based rather than merely selection-based responses and by extending the work into additional relations, including nonsymmetrical ones. In each of the four studies participants pretrained in contextual control over nonarbitrary stimulus relations of sameness and opposition, or of sameness, smaller than, and larger than, learned arbitrary stimulus relations in the presence of these relational cues and derived analogies involving directly trained relations and derived relations of mutual and combinatorial entailment, measured using a variety of productive and selection-based measures. In Experiment 1 participants successfully recognized analogies among stimulus networks containing same and opposite relations; in Experiment 2 analogy was successfully used to extend derived relations to pairs of novel stimuli; in Experiment 3 the procedure used in Experiment 1 was extended to nonsymmetrical comparative relations; in Experiment 4 the procedure used in Experiment 2 was extended to nonsymmetrical comparative relations. Although not every participant showed the effects predicted, overall the procedures occasioned relational responses consistent with an RFT account that have not yet been demonstrated in a behavior-analytic laboratory setting, including productive responding on the basis of analogies.

Lipkens, Regina; Hayes, Steven C

2009-01-01

275

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

276

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?  

PubMed Central

Background Retrotransposons are key players in the evolution of eukaryotic genomes. Moreover, it is now known that some retrotransposon classes, like the abundant and plant-specific Sireviruses, have intriguingly distinctive host preferences. Yet, it is largely unknown if this bias is supported by different genome structures. Results We performed sensitive comparative analysis of the genomes of a large set of Ty1/copia retrotransposons. We discovered that Sireviruses are unique among Pseudoviridae in that they constitute an ancient genus characterized by vastly divergent members, which however contain highly conserved motifs in key non-coding regions: multiple polypurine tract (PPT) copies cluster upstream of the 3' long terminal repeat (3'LTR), of which the terminal PPT tethers to a distinctive attachment site and is flanked by a precisely positioned inverted repeat. Their LTRs possess a novel type of repeated motif (RM) defined by its exceptionally high copy number, symmetry and core CGG-CCG signature. These RM boxes form CpG islands and lie a short distance upstream of a conserved promoter region thus hinting towards regulatory functions. Intriguingly, in the envelope-containing Sireviruses additional boxes cluster at the 5' vicinity of the envelope. The 5'LTR/internal domain junction and a polyC-rich integrase signal are also highly conserved domains of the Sirevirus genome. Conclusions Our comparative analysis of retrotransposon genomes using advanced in silico methods highlighted the unique genome organization of Sireviruses. Their structure may dictate a life cycle with different regulation and transmission strategy compared to other Pseudoviridae, which may contribute towards their pattern of distribution within and across plants.

2010-01-01

277

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

278

Conservation of the Conformation and Positive Charges of Hepatitis C Virus E2 Envelope Glycoprotein Hypervariable Region 1 Points to a Role in Cell Attachment  

PubMed Central

Chronic hepatitis C virus (HCV) infection is a major cause of liver disease. The HCV polyprotein contains a hypervariable region (HVR1) located at the N terminus of the second envelope glycoprotein E2. The strong variability of this 27-amino-acid region is due to its apparent tolerance of amino acid substitutions together with strong selection pressures exerted by anti-HCV immune responses. No specific function has so far been attributed to HVR1. However, its presence at the surface of the viral particle suggests that it might be involved in viral entry. This would imply that HVR1 is not randomly variable. We sequenced 460 HVR1 clones isolated at various times from six HCV-infected patients receiving alpha interferon therapy (which exerts strong pressure towards quasispecies genetic evolution) and analyzed their amino acid sequences together with those of 1,382 nonredundant HVR1 sequences collected from the EMBL database. We found that (i) despite strong amino acid sequence variability related to strong pressures towards change, the chemicophysical properties and conformation of HVR1 were highly conserved, and (ii) HVR1 is a globally basic stretch, with the basic residues located at specific sequence positions. This conservation of positively charged residues indicates that HVR1 is involved in interactions with negatively charged molecules such as lipids, proteins, or glycosaminoglycans (GAGs). As with many other viruses, possible interaction with GAGs probably plays a role in host cell recognition and attachment.

Penin, Francois; Combet, Christophe; Germanidis, Georgios; Frainais, Pierre-Olivier; Deleage, Gilbert; Pawlotsky, Jean-Michel

2001-01-01

279

Long-Range Comparison of Human and Mouse SCL Loci: Localized Regions of Sensitivity to Restriction Endonucleases Correspond Precisely with Peaks of Conserved Noncoding Sequences  

PubMed Central

Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by the SIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream from MAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.

Gottgens, Berthold; Gilbert, James G.R.; Barton, Linda M.; Grafham, Darren; Rogers, Jane; Bentley, David R.; Green, Anthony R.

2001-01-01

280

Conserved hydrophobic amino acid residues in the N-terminal region of DnaA protein are involved in DnaA-DnaA interaction.  

PubMed

We previously reported that a leucine-zipper-like structure (I26, L33 and L40) located in the N-terminal region of DnaA is essential for the duplex opening at oriC by DnaA. In this study, we focused on three other conserved hydrophobic amino acid residues, L3, L10 and L17, and examined the function of DnaA proteins mutated in these amino acid residues. DnaA427 (L17S) and DnaA413 (L3S, L10S and L17S) were inactive for oriC DNA replication both in vitro and in vivo. Although these mutant DnaA proteins maintained their binding activities for both ATP and oriC, they were unable to induce the opening of duplex DNA at oriC. Glutathione-S-transferase (GST)-fused wild-type DnaA interacted with wild-type DnaA but not with DnaA427 and DnaA413. Based on these results, we propose that conserved hydrophobic amino acid residues in the N-terminal region of DnaA are involved in DnaA oligomerization, in which DnaA-DnaA interaction is required. PMID:11945177

Mima, Shinji; Makise, Masaki; Koterasawa, Motohiro; Tsuchiya, Tomofusa; Mizushima, Tohru

2002-08-01

281

Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation  

PubMed Central

Background Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. Results A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. Conclusion Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.

Armstead, Ian; Huang, Lin; King, Julie; Ougham, Helen; Thomas, Howard; King, Ian

2007-01-01

282

Expression of human TFIIA subunits in Saccharomyces cerevisiae identifies regions with conserved and species-specific functions.  

PubMed

The transcription factor TFIIA stabilizes the interaction between the TATA-binding protein (TBP) and promoter DNA and facilitates activator function. In yeast, TFIIA is composed of large (TOA1) and small (TOA2) subunits that interact to form a beta-barrel domain and a helix bundle domain. Here we report plasmid shuffle experiments showing that the human subunits (TFIIAalpha/beta, ALF, and TFIIAgamma) are not able to support growth in yeast and that the failure is associated with morphological abnormalities related to cell division. To determine the regions responsible for species specificity, we examined a series of chimeric yeast-human subunits. The results showed that yeast-human hybrids that contained the N-termini of TFIIAgamma or TFIIAalpha/beta were viable, presumably because they could form a functional interspecies alpha-helical bundle. Likewise, a TOA1 hybrid that contained the nonconserved internal region from TFIIAalpha/beta also had no effect on TFIIA function. However, hybrids that contained the acidic region III or C-terminal region IV from TFIIAalpha/beta grew more slowly than the wild-type TOA1 subunit, and if both regions were exchanged, this effect was far more severe. Although these hybrids exchanged sequences which are involved in beta-barrel formation and interactions with TBP, they were all active in a TBP-dependent mobility shift assay. The results suggest that the growth phenotypes of these hybrids might be due to a failure to interact with components of the yeast transcription machinery other than TBP. Finally, we show that sequences from region III of TFIIA large subunits fall into classes that are either highly acidic or that are divergent and nonacidic, and provide the first evidence to suggest that, at least in yeast, this region is important for TFIIA function. PMID:12527429

Upadhyaya, Ashok B; DeJong, Jeff

2003-01-01

283

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

284

Disorder targets misorder in nuclear quality control degradation: a disordered ubiquitin ligase directly recognizes its misfolded substrates  

PubMed Central

Summary Protein quality control (PQC) degradation systems protect the cell from the toxic accumulation of misfolded proteins. Because any protein can become misfolded, these systems must be able to distinguish abnormal proteins from normal ones, yet be capable of recognizing the wide variety of distinctly shaped misfolded proteins they are likely to encounter. How individual PQC degradation systems accomplish this remains an open question. Here we show that the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains. These disordered domains are punctuated with small segments of order and high sequence conservation that serve as substrate-recognition sites San1 uses to target its different substrates. We propose that these substrate-recognition sites, interspersed among flexible, disordered regions, provide San1 an inherent plasticity that allows it to bind its many, differently shaped misfolded substrates.

Rosenbaum, Joel C.; Fredrickson, Eric K.; Oeser, Michelle L.; Garrett-Engele, Carrie M.; Locke, Melissa N.; Richardson, Lauren A.; Nelson, Zara W.; Hetrick, Elizabeth D.; Milac, Thomas I.; Gottschling, Daniel E.; Gardner, Richard G.

2011-01-01

285

The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae)  

Microsoft Academic Search

The identification of genomic regions with sufficient variation to elucidate fine-scale relationships among closely related species is a major goal of phylogenetic systematics. However, the accumulation of such multi-locus data sets brings its own challenges, given that gene trees do not necessarily represent the true species tree. Using genomic tools developed for Solanum (Solanaceae), we have evaluated the utility of

Rachel A. Levin; Andrew Whelan; Jill S. Miller

2009-01-01

286

The presence of inhibitory RNA elements in the late 3?-untranslated region is a conserved property of human papillomaviruses  

Microsoft Academic Search

Here we have tested the inhibitory activity of the late untranslated region (UTR) of nine different human papillomavirus (HPV) types representing three different genera and six different species. These HPVs include both low-risk and high-risk types. We found that the late UTR of the various HPVs all displayed inhibitory activity, although they inhibited gene expression to various extent. The late

Xiaomin Zhao; Margaret Rush; Anette Carlsson; Stefan Schwartz

2007-01-01

287

Patterns of development and conservation in agricultural lands—The case of the Tel Aviv metropolitan region 1990–2000  

Microsoft Academic Search

Until the 1990s Israel was implementing a strict agricultural land preservation policy program, rooted in Zionist ideology. This was changed when shifts in Israeli planning and land policy towards the end of the 20th century brought about accelerated growth and sprawling development in agricultural lands at the urban–rural fringe, particularly in the Tel Aviv metropolitan region (TMR). In this article

Tseira Maruani; Irit Amit-Cohen

2010-01-01

288

Conservation tillage issues: cover crop-based organic rotational no-till grain production in the mid-atlantic region  

Technology Transfer Automated Retrieval System (TEKTRAN)

Organic producers in the mid-Atlantic region are interested in reducing tillage, labor, and time requirements for grain production. Cover crop-based organic rotational no-till grain production is one approach to accomplishing these goals. Advancements in a system for planting crops into a mat of cov...

289

Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs  

PubMed Central

Background Trypanosomatids exhibit a unique gene organization into large directional gene clusters (DGCs) in opposite directions. The transcription "strand switch region" (SSR) separating the two large DGCs that constitute chromosome 1 of Leishmania major has been the subject of several studies and speculations. Thus, it has been suspected of being the single replication origin of the chromosome, the transcription initiation site for both DGCs or even a centromere. Here, we have used an inter-species compared genomics approach on this locus in order to try to identify conserved features or motifs indicative of a putative function. Results We isolated, and compared the structure and nucleotide sequence of, this SSR in 15 widely divergent species of Leishmania and Sauroleishmania. As regards its intrachromosomal position, size and AT content, the general structure of this SSR appears extremely stable among species, which is another demonstration of the remarkable structural stability of these genomes at the evolutionary level. Sequence alignments showed several interesting features. Overall, only 30% of nucleotide positions were conserved in the SSR among the 15 species, versus 74% and 62% in the 5' parts of the adjacent XPP and PAXP genes, respectively. However, nucleotide divergences were not distributed homogeneously along this sequence. Thus, a central fragment of approximately 440 bp exhibited 54% of identity among the 15 species. This fragment actually represents a new Leishmania-specific CDS of unknown function which had been overlooked since the annotation of this chromosome. The encoded protein comprises two trans-membrane domains and is classified in the "structural protein" GO category. We cloned this novel gene and expressed it as a recombinant green fluorescent protein-fused version, which showed its localisation to the endoplasmic reticulum. The whole of these data shorten the actual SSR to an 887-bp segment as compared with the original 1.6 kb. In the rest of the SSR, the percentage of identity was much lower, around 22%. Interestingly, the 72-bp fragment where the putatively single transcription initiation site of chromosome 1 was identified is located in a low-conservation portion of the SSR and is itself highly polymorphic amongst species. Nevertheless, it is highly C-rich and presents a unique poly(C) tract in the same position in all species. Conclusion This inter-specific comparative study, the first of its kind, (a) allowed to reveal a novel genus-specific gene and (b) identified a conserved poly(C) tract in the otherwise highly polymorphic region containing the putative transcription initiation site. This allows hypothesising an intervention of poly(C)-binding proteins known elsewhere to be involved in transcriptional control.

Puechberty, Jacques; Blaineau, Christine; Meghamla, Sabrina; Crobu, Lucien; Pages, Michel; Bastien, Patrick

2007-01-01

290

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

291

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns  

PubMed Central

Background Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Results Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Conclusions Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

2011-01-01

292

Agroforestry for soil and water conservation in the western Himalayan Valley Region of India 2. Crop and tree production  

Microsoft Academic Search

A ten-year-study (1983 to 1992) conducted on nine 15 90 m runoff plots at 4% slope compared production efficiency of Leucaena\\u000a leucocephala and Eucalyptus hybrid based agroforestry as well as monocropping landuse systems in the warm, subhumid climate\\u000a of the western Himalayan region of India. Treatments for the first sequence were: monocropping systems of leucaena, eucalyptus,\\u000a Chrysopogon fulvus grass and

Pratap Narain; R. K. Singh; N. S. Sindhwal; P. Joshie

1997-01-01

293

Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch.  

PubMed

Conformational dynamics and observed equilibrium constants for ligand binding of the adenine-specific riboswitch (add-A riboswitch) in the absence of Mg(2+) and presence of various concentrations of poly-ethylene glycol having an average molecular weight of 200 indicated that 54.2 water molecules were released from P2 and P3 stem regions of the add-A riboswitch during conformational transition upon the binding of 2-aminopurine, an analog of the natural ligand adenine. PMID:22854864

Kumar, Vinit; Endoh, Tamaki; Murakami, Kentaro; Sugimoto, Naoki

2012-10-01

294

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

Microsoft Academic Search

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

Martin Kircher; Christoph Bock; Martina Paulsen

2008-01-01

295

Recognizing Mantle Plumes in the Geological Record  

NASA Astrophysics Data System (ADS)

Mantle plumes are recognized by domal uplift, triple junction rifting, and especially the presence of a large igneous province (LIP), dominated in the Phanerozoic by flood basalts, and in the Proterozoic by the exposed plumbing system of dykes, sills, and layered intrusions. In the Archean, greenstone belts that contain komatiites have been linked to plumes. In addition, some carbonatites and kimberlites may originate from plumes that have stalled beneath thick lithosphere. Geochemistry and isotopes can be used to test and characterize the plume origin of LIPs. Seismic tomography and geochemistry of crustal and subcrustal xenoliths in kimberlites can identify fossil plumes. More speculatively, plumes (or clusters of plumes) have been linked with variation in the isotopic composition of marine carbonates, sea-level rise, iron formations, anoxia events, extinctions, continental breakup, juvenile crust production, magnetic superchrons, and meteorite impacts. The central region of a plume is located using the focus of a radiating dyke swarm, the distribution of komatiites and picrites, etc. The outer boundary of a plume head circumscribes the main flood basalt distribution and approximately coincides with the edge of domal uplift that causes shoaling and offlap in regional sedimentation.

Ernst, Richard E.

296

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

297

Sequence conservation in the rRNA first internal transcribed spacer region of Babesia gibsoni genotype Asia isolates.  

PubMed

Babesia gibsoni genotype Asia is a small, tick-transmitted intraerythrocytic protozoan that parasitizes dogs. Reports suggest that it is increasingly diagnosed in the United States. The clinical outcome of infection with this piroplasm is often variable, leading us to hypothesize that the different clinical outcomes resulting from B. gibsoni genotype Asia infection are due to genetically distinguishable strains that differ in virulence. As a first step to assess the genetic variability of B. gibsoni isolates originating from the southeastern United States, we sequenced the rRNA first internal transcribed spacer region of recent isolates from Georgia and Alabama, and compared these sequences with isolates originating from Japan and Australia. All isolates examined proved to be genetically identical at the first internal transcribed spacer region, although this region differed distinctly from other Babesia species and closely related apicomplexan species. Although negating our hypothesis, this information gives us insight into the recent evolutionary history and spread of B. gibsoni genotype Asia in dogs in the U.S. Our research suggests that the gradual rise in prevalence of canine babesiosis due to B. gibsoni genotype Asia in the United States may be a result of clonal expansion of a single strain within a susceptible host population. PMID:18207327

Bostrom, B; Wolf, C; Greene, C; Peterson, D S

2007-12-08

298

Pub1p C-Terminal RRM Domain Interacts with Tif4631p through a Conserved Region Neighbouring the Pab1p Binding Site  

PubMed Central

Pub1p, a highly abundant poly(A)+ mRNA binding protein in Saccharomyces cerevisiae, influences the stability and translational control of many cellular transcripts, particularly under some types of environmental stresses. We have studied the structure, RNA and protein recognition modes of different Pub1p constructs by NMR spectroscopy. The structure of the C-terminal RRM domain (RRM3) shows a non-canonical N-terminal helix that packs against the canonical RRM fold in an original fashion. This structural trait is conserved in Pub1p metazoan homologues, the TIA-1 family, defining a new class of RRM-type domains that we propose to name TRRM (TIA-1 C-terminal domain-like RRM). Pub1p TRRM and the N-terminal RRM1-RRM2 tandem bind RNA with high selectivity for U-rich sequences, with TRRM showing additional preference for UA-rich ones. RNA-mediated chemical shift changes map to ?-sheet and protein loops in the three RRMs. Additionally, NMR titration and biochemical in vitro cross-linking experiments determined that Pub1p TRRM interacts specifically with the N-terminal region (1–402) of yeast eIF4G1 (Tif4631p), very likely through the conserved Box1, a short sequence motif neighbouring the Pab1p binding site in Tif4631p. The interaction involves conserved residues of Pub1p TRRM, which define a protein interface that mirrors the Pab1p-Tif4631p binding mode. Neither protein nor RNA recognition involves the novel N-terminal helix, whose functional role remains unclear. By integrating these new results with the current knowledge about Pub1p, we proposed different mechanisms of Pub1p recruitment to the mRNPs and Pub1p-mediated mRNA stabilization in which the Pub1p/Tif4631p interaction would play an important role.

Rico-Lastres, Palma; Perez-Canadillas, Jose Manuel

2011-01-01

299

Glucose-mediated transactivation of carbohydrate response element-binding protein requires cooperative actions from Mondo conserved regions and essential trans-acting factor 14-3-3.  

PubMed

Carbohydrate response element-binding protein (ChREBP) is a basic helix-loop-helix/leucine zipper transcription factor that binds to the carbohydrate response element in the promoter of certain lipogenic and glycolytic genes. High glucose can activate ChREBP by releasing an intramolecular inhibition within the glucose-sensing module (GSM) that occurs in low glucose. We report here that the glucose response of GSM is mediated by cooperation between five conserved submodules known as Mondo conserved regions (MCRs) I through V within GSM. Deletion of individual MCRs leads to complete (for MCR II, III, and IV) or partial (MCR I) loss of glucose response of ChREBP. MCR IV is necessary and sufficient for inhibiting the transcriptional activity of ChREBP under low glucose. The roles of MCR II and III in glucose response of ChREBP are independent of and distinct from their function in controlling subcellular localization. We further demonstrate that, instead of inhibiting ChREBP activity as would be predicted from its cytoplasmic retentive function, 14-3-3 binding with MCR III is essential for the glucose responsiveness of ChREBP. The interaction between 14-3-3 and ChREBP is constitutive, indicating a permissive role of 14-3-3 in the glucose response of ChREBP. We further uncovered an unconventional 14-3-3 binding motif (residues 116-135) lacking phosphor-serine/threonine within MCR III, a predicted alpha-helix highly conserved in all Mondo proteins. We conclude that individual subdomains in the GSM (MCR I through V) play diverse but crucial roles in cooperation with essential trans-acting cofactors such as 14-3-3 proteins to mediate the glucose response of ChREBP. PMID:18436566

Li, Ming V; Chen, Weiqin; Poungvarin, Naravat; Imamura, Minako; Chan, Lawrence

2008-04-24

300

Glucose-Mediated Transactivation of Carbohydrate Response Element-Binding Protein Requires Cooperative Actions from Mondo Conserved Regions and Essential Trans-Acting Factor 14-3-3  

PubMed Central

Carbohydrate response element-binding protein (ChREBP) is a basic helix-loop-helix/leucine zipper transcription factor that binds to the carbohydrate response element in the promoter of certain lipogenic and glycolytic genes. High glucose can activate ChREBP by releasing an intramolecular inhibition within the glucose-sensing module (GSM) that occurs in low glucose. We report here that the glucose response of GSM is mediated by cooperation between five conserved submodules known as Mondo conserved regions (MCRs) I through V within GSM. Deletion of individual MCRs leads to complete (for MCR II, III, and IV) or partial (MCR I) loss of glucose response of ChREBP. MCR IV is necessary and sufficient for inhibiting the transcriptional activity of ChREBP under low glucose. The roles of MCR II and III in glucose response of ChREBP are independent of and distinct from their function in controlling subcellular localization. We further demonstrate that, instead of inhibiting ChREBP activity as would be predicted from its cytoplasmic retentive function, 14-3-3 binding with MCR III is essential for the glucose responsiveness of ChREBP. The interaction between 14-3-3 and ChREBP is constitutive, indicating a permissive role of 14-3-3 in the glucose response of ChREBP. We further uncovered an unconventional 14-3-3 binding motif (residues 116–135) lacking phosphor-serine/threonine within MCR III, a predicted ?-helix highly conserved in all Mondo proteins. We conclude that individual subdomains in the GSM (MCR I through V) play diverse but crucial roles in cooperation with essential trans-acting cofactors such as 14-3-3 proteins to mediate the glucose response of ChREBP.

Li, Ming V.; Chen, Weiqin; Poungvarin, Naravat; Imamura, Minako; Chan, Lawrence

2008-01-01

301

Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds  

PubMed Central

Background Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1) is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1) locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds. Results Three highly conserved regions (HMCO1-3) were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9?kb region located ~70?kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1), is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1 genomic landscape locate to the DNAse I hypersensitive sites identified in this genomic region by the ENCODE consortium. Conclusions This study establishes that distant cis-regulatory regions scattered through a larger genomic landscape control the highly dynamic expression of Grem1, which is key to normal progression of mouse limb bud development.

2012-01-01

302

Amino acid changes in the fourth conserved region of human immunodeficiency virus type 2 strain HIV-2ROD envelope glycoprotein modulate fusion.  

PubMed Central

The fourth conserved region (C4) of human immunodeficiency virus type 1 (HIV-1) surface glycoprotein has been shown to participate in CD4 binding and to influence viral tropism (A. Cordonnier, L. Montagnier, and M. Emerman, Nature [London] 340:571-574, 1989). To define the role of the corresponding region of HIV-2, we introduce single amino acid changes into the C4 sequence of HIV-2ROD. The effects of these mutations on glycoprotein function and on virus infectivity have been examined. We have shown that the tryptophan residue at position 428 is necessary primarily for CD4 binding. The isoleucine residue at position 421 is necessary for the establishment of productive infection in the promonocytic cell line U937, while it is dispensable to some extent for infection of primary T lymphocytes or the lymphocytic cell line SUP-T1. This replication defect correlated with the failure of the Ile-421-to-Thr (Ile-421-->Thr) mutant glycoprotein to form syncytia in U937 cells. DNA analysis of revertant viruses revealed that a strong selective pressure was exerted on residue 421 of the surface glycoprotein to allow HIV-2 infection of U937 cells. These results demonstrate that this region of HIV-2 plays an important role in determining fusion efficiency in a cell-dependent manner and consequently can influence viral tropism. Images

Keller, R; Peden, K; Paulous, S; Montagnier, L; Cordonnier, A

1993-01-01

303

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

304

Using Nodal Ratios to Predict Risk of Regional Recurrences in Patients Treated with Breast Conservation Therapy with 4 or More Positive Lymph Nodes  

PubMed Central

Purpose. The value of nodal ratios (NRs) as a prognostic variable in breast cancer is continually being demonstrated. The purpose of this study was to use NR in patients with ?4+ nodes to assess a correlation of NR with regional (lymph node) recurrence. Methods. Inclusion criteria was ?8 nodes dissected with ?4+ nodes after breast conservation therapy. Of 1060 patients treated from 1975 to 2003 who had a minimum of 8 nodes dissected, 273 were node+; 56 patients had ?4+ involved nodes and were the focus of this study. Nodal ratios were calculated for each patient and grouped into 3 categories: high (?70%), intermediate (40%–69%) and low (<40%). Each nodal ratio was correlated with patterns of local, regional, and distant failures and OS. Results. Outcomes for the entire cohort were BRFS-83%, NRFS-93%, DMFS-61%, and OS 63% at 10 yrs. The OS, DMFS, and NRFS correlated with N2 (4–9 nodes+) versus N3 (?10+) status but did not correlate with BRFS, as expected. When evaluating NR, 18 pts had high NR (>70%). Only 3 patients experienced nodal recurrences, all within previously radiated supraclavicular fields. All 3 in-field regional failures occurred in the N3 group of patients with NR >70%. All were treated with a single AP field prescribed to a dose of 46 Gy at a standard depth of 3 cm. Conclusions. In this group of N2/N3 patients treated with BCT, we were able to identify patients at high risk for regional failures as those with high NR of >70% and ?10+ nodes. While these findings need to be reproduced in larger datasets, this group of patients with NR of >70% in 4 or more positive axillary lymph nodes may benefit from meticulous targeting of regional nodes, dose escalation, and/or more intensive systemic therapies.

Castrucci, William; Lannin, Donald; Haffty, Bruce G.; Higgins, Susan A.; Moran, Meena S.

2011-01-01

305

Mapping of the KHSRP gene to a region of conserved synteny on human chromosome 19p13.3 and mouse chromosome 17.  

PubMed

The K homology-type splicing regulatory protein, KSRP, activates splicing through intronic splicing enhancer sequences. It is highly expressed in neural cells and is required for the neural-specific splicing of the c-src N1 exon. In this study, we mapped the gene (gene symbols KHSRP and Khsrp) to human chromosome 19 by using radiation hybrid panels and to mouse chromosome 17 by studying an interspecific backcross panel. Human KHSRP is a positional candidate gene for familial febrile convulsion and Cayman type cerebellar ataxia. Comparative analysis of the human and mouse genomes indicates that the KHSRP gene is located in regions of conserved synteny between the two species. PMID:10087204

Ring, H Z; Vameghi-Meyers, V; Nikolic, J M; Min, H; Black, D L; Francke, U

1999-03-15

306

Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation.  

PubMed Central

The retinoid X receptor (RXR) participates in a wide array of hormonal signaling pathways, either as a homodimer or as a heterodimer, with other members of the steroid and thyroid hormone receptor superfamily. In this report the ligand-dependent transactivation function of RXR has been characterized, and the ability of RXR to interact with components of the basal transcription machinery has been examined. In vivo and in vitro experiments indicate the RXR ligand-binding domain makes a direct, specific, and ligand-dependent contact with a highly conserved region of the TATA-binding protein. The ability of mutations that reduce ligand-dependent transcription by RXR to disrupt the RXR-TATA-binding protein interaction in vivo and in vitro suggests that RXR makes direct contact with the basal transcription machinery to achieve activation. Images Fig. 3

Schulman, I G; Chakravarti, D; Juguilon, H; Romo, A; Evans, R M

1995-01-01

307

The Thai Phase III HIV Type 1 Vaccine Trial (RV144) Regimen Induces Antibodies That Target Conserved Regions Within the V2 Loop of gp120  

PubMed Central

Abstract The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200–3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100–200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169–184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100–800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100–3200) and 3570 (range: 200–12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition.

Billings, Erik; Rao, Mangala; Williams, Constance; Zolla-Pazner, Susan; Bailer, Robert T.; Koup, Richard A.; Madnote, Sirinan; Arworn, Duangnapa; Shen, Xiaoying; Tomaras, Georgia D.; Currier, Jeffrey R.; Jiang, Mike; Magaret, Craig; Andrews, Charla; Gottardo, Raphael; Gilbert, Peter; Cardozo, Timothy J.; Rerks-Ngarm, Supachai; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Paris, Robert; Greene, Kelli; Gao, Hongmei; Gurunathan, Sanjay; Tartaglia, Jim; Sinangil, Faruk; Korber, Bette T.; Montefiori, David C.; Mascola, John R.; Robb, Merlin L.; Haynes, Barton F.; Ngauy, Viseth; Michael, Nelson L.; Kim, Jerome H.; de Souza, Mark S.

2012-01-01

308

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

PubMed Central

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

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

2012-01-01

309

STRUCTURE OF THE LA MOTIF: A WINGED HELIX DOMAIN MEDIATES RNA BINDING VIA A CONSERVED AROMATIC PATCH  

Microsoft Academic Search

The La protein is a ubiquitous nuclear phosphoprotein that recognizes the 30 uridylates found in all newly synthe- sized RNA polymerase III transcripts. La binding stabilizes these transcripts from exonucleases and may also assist their folding. Here we present the first structural insights into how the La protein specifically interacts with its RNA substrates. The most conserved region of the

Gang Dong; Ghadiyaram Chakshusmathi; Sandra L Wolin; Karin M Reinisch

2004-01-01

310

Engineering support vector machine kernels that recognize translation initiation sites  

Microsoft Academic Search

Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show

Alexander Zien; Gunnar Rätsch; Sebastian Mika; Bernhard Schölkopf; Thomas Lengauer; Klaus-robert Müller

2000-01-01

311

Engineering Support Vector Machine Kerneis That Recognize Translation Initialion Sites  

Microsoft Academic Search

In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points from which regions encoding pro- teins start, the so-called translation initiation sites (TIS). This can be modeled as a classification prob- lem. We demonstrate the power of support vector machines (SVMs) for this task, and show how to suc- cessfully incorporate biological prior

Alexander Zien; Gunnar Rätsch; Sebastian Mika; Bernhard Schölkopf; Christian Lemmen; Alex J. Smola; Thomas Lengauer; Klaus-robert Müller

1999-01-01

312

Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites  

Microsoft Academic Search

Motivation: In order to extract protein sequences from nu- cleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a clas- sification problem. We demonstrate the applicability of sup- port vector machines (SVMs) for

A. Zien; G. Ratsch; S. Mika; B. Sch

313

Bat assemblages in conservation areas of a metropolitan region in Southeastern Brazil, including an important karst habitat.  

PubMed

Species richness and abundance of bats were studied in four nature reserves, including a karst area which has many potential rocky shelters for bats, such as caves and rock crevices. The reserves were located in the greater Belo Horizonte metropolitan area, one of the most populated regions of Brazil, within the Atlantic Forest, and Cerrado (Brazilian savanna) ecological domains. Bats were sampled using mist-nets and, in the karst area, also by active searches in shelters. A total of 1,599 bats were captured representing 30 species belonging to four families. There was little similarity among the four chiropteran faunas. The greatest species richness was found in the karst area with 22 species recorded whereas richness estimates in the other areas indicated the need for further studies. Two hundred and sixty-five individuals of 14 species were captured from 56 shelters. Most of the shelters were frequently used for diurnal roosts, and all the bats found belonged to the Phyllostomidae, with the exception of Myotis nigricans (Vespertilionidae), Nyctinomops laticaudatus (Molossidae) and Peropteryx macrotis (Emballonuridae). The sanguinivorous Desmodus rotundus was the most common species in the shelters. The results of this study demonstrate the importance of maintaining multiple protected areas to ensure a representative fauna of bats in a region characterized by a vegetation transition zone and with intense economic activity and high environmental impact. This study also demonstrates the importance of rock shelters for maintaining local bat richness and the importance of active searches for bats in their diurnal roosts for a more thorough sampling of the bat fauna at a given locality. PMID:23917558

Talamoni, S A; Coelho, D A; Dias-Silva, L H; Amaral, A S

2013-05-01

314

Recognizing speech of goats, wolves, sheep and ... non-natives  

Microsoft Academic Search

This paper reviews the current understanding of acoustic–phonetic issues and the problems arising when trying to recognize speech from non-native speakers. Conceptually, regional accents are well modeled by systematic shifts in pronunciation. Therefore, simultaneous recognition of multiple regional variants may be performed by using multiple acoustic models in parallel, or by adding pronunciation variants in the dictionary. Recognition of non-native

Dirk Van Compernolle

2001-01-01

315

Monoclonal antibodies recognize gly-leu-phe-gly repeat of nucleoporin nup98 of tetrahymena, yeasts, and humans.  

PubMed

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. PMID:23607342

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

2013-04-01

316

A performance comparison of two handwriting recognizers  

Microsoft Academic Search

An experiment is described comparing two commercial handwriting recognizers with discrete hand-printed characters. Each recognizer was tested at two levels of constraint, one using lowercase letters (which were the only symbols included in the input text) and the other using both uppercase and lowercase letters. Two factors—recognizer and constraint—with two levels each, resulted in four test conditions. A total of

I. Scott Mackenzie; Larry Chang

1999-01-01

317

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

PubMed Central

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.

Weber, Kristina; Zuschin, Martin

2013-01-01

318

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...

319

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

320

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

321

Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region.  

PubMed Central

U1 is a small non-polyadenylated nuclear RNA that is transcribed by RNA polymerase II and is known to play a role in mRNA splicing. The mature 3' end of U1 snRNA is formed in at least two steps. The first step generates precursors of U1 RNA with a few extra nucleotides at the 3' end; in the second step, these precursors are shortened to mature U1 RNA. Here, I have determined the sequences required for the first step. Human U1 genes with various deletions and substitutions near the 3' end of the coding region were constructed and introduced into HeLa cells by DNA transfection. The structure of the RNA synthesized during transient expression of the exogenous U1 gene was analyzed by S1 mapping. The results show that a 13 nucleotide sequence located downstream from the U1 coding region and conserved among U1, U2 and U3 genes of different species is the only sequence required to direct the first step in the formation of the 3' end of U1 snRNA. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8.

Hernandez, N

1985-01-01

322

The Conserved N-Terminal Region of the Mitotic Checkpoint Protein BUBR1: A Putative TPR Motif of High Surface Activity  

PubMed Central

BUBR1, a key component of the mitotic spindle checkpoint, is a multidomain protein kinase that is activated in response to kinetochore tension. Although BUB1 and BUBR1 play an important role in cell division, very little is known about their structural characteristics. We show that the conserved N-terminal region of BUBR1, comprising residues 1–204, is a globular domain of high ?-helical content (?60%), stable in the pH range 4–9 and probably organized as a tetratricopeptide motif repeat (TPR), most closely resembling residues 16–181 of protein phosphatase 5. Because the latter presents a continuous amphipathic groove and is regulated by binding certain fatty acids, we compared the properties of BUBR1(1–204) and TPR-PP5(16–181) at air/water interfaces and found that both proteins exhibited a similar surface activity and formed stable, rigid monolayers. The deletion of a region that probably comprises several ?-helices of BUBR1 indicates that long-range interactions are essential for the stability of the N-terminal domain. The presence of the putative TPR motif strongly suggests that the N-terminal domain of BUBR1 is involved in direct protein-protein interactions and/or protein-lipid interactions.

Bolanos-Garcia, V. M.; Beaufils, S.; Renault, A.; Grossmann, J. G.; Brewerton, S.; Lee, M.; Venkitaraman, A.; Blundell, T. L.

2005-01-01

323

Growth hormone transcription factor ZN-16 genomic coding regions are composed of a single exon and are evolutionarily conserved in mammals.  

PubMed

The structure of the gene encoding ZN-16, a transcription factor that binds to the mammalian growth hormone promoter in tandem with Pit-1, was determined in order to elucidate the exon-intron organization of the 16 zinc finger domains of the protein. Southern hybridization of mouse genomic DNA showed fragments with sizes identical to those predicted from mouse ZN-16 cDNA for two different probes covering the 2200 aa coding frame. Mouse genome database sequences also showed no introns in the zn-16 coding regions on chromosome 4. Analysis of human zn-16 by Southern hybridization and genomic database sequence analysis also indicated a single exon for the human protein coding sequences. BLASTP query of available genomic databases with critical zinc finger residues from mouse ZN-16 identified highly similar canine, bovine, and chimpanzee genomic sequences that encode proteins. Phylogenetic analysis of these mammalian proteins resulted in relationships as would be expected in species spanning rodents to humans. All six independent zn-16 sequences show a single exon coding region with no introns, a similarity ruling out the possibility that these genomic sequences are pseudogenes. Thus, mammalian zn-16 has a compact single exon structure encoding a very large protein (2200-3000 aa), the conservation of which may have functional implications such as the importance of posttranscriptional modifications. PMID:16303260

Flynn, Maxfield P; Hurley, David L

2005-11-21

324

Optional exon in the 5'-untranslated region of 3-hydroxy-3-methylglutaryl coenzyme A synthase gene: conserved sequence and splicing pattern in humans and hamsters  

SciTech Connect

3-Hydroxy-3-methylglutaryl coenzyme A synthase (hydroxymethylglutaryl-CoA synthase, EC 4.1.3.5) is a negatively regulated enzyme in the synthetic pathway for cholesterol, isopentenyl tRNA, and other isoprenoids. The 5'-untranslated region of the mRNA for Chinese hamster hydroxymethylglutaryl-CoA synthase contains an optional exon of 59 nucleotides located 10 nucleotides upstream of the translation start site. About 50% of the mRNAs contain this exon, and the other 50% lack it owing to differential intron splicing. The authors show that the two transcripts are found in similar ratios in multiple tissues of the Syrian hamster, including the brain. The relative amounts of the two transcripts in brain and liver are constant from day 0 to day 75 of life. A similar alternative splicing pattern for hydroxymethylglutaryl-CoA synthase was observed in three human tissues: cultured fibroblasts, fetal adrenal gland, and fetal liver. A cDNA for human synthase had 90% homology to the hamster sequence in the region corresponding to the optional exon. This sequence contains a 20 out of 26 nucleotide match with the sequence immediately upstream of the initiator AUG codon in the mRNA for hamster hydroxymethylglutaryl-CoA reductase, the enzyme that follows the synthase in the isoprenoid biosynthetic pathway. These findings raise the possibility that the optional exon plays an important, conserved functional role in humans and hamsters.

Gil, G.; Smith, J.R.; Goldstein, J.L.; Brown, M.S.

1987-04-01

325

Willingness To Pay For Systematic Management Of Community Forests For Conservation Of Non-Timber Forest Products In Nigeria’s Rainforest Region  

Microsoft Academic Search

Despite the importance of non-timber forest products (NTFP) in sustaining livelihood and poverty smoothening in rural communities,\\u000a they are highly depleted and poorly conserved. Besides, conservation initiatives in Nigeria to date are rarely participatory.\\u000a Even community forests, the main source of NTFP, are poorly conserved. Therefore, to enhance participatory conservation initiatives,\\u000a this study determines the willingness of households in forest

Nnaemeka A. Chukwuone; Chukwuemeka E. Okorji

326

Structurally defined epitopes of Haemophilus ducreyi lipooligosaccharides recognized by monoclonal antibodies.  

PubMed Central

By use of enzyme-linked immunosorbent assay and immunoblotting techniques, the migration patterns and binding epitopes of lipooligosaccharides (LOS) from 10 Haemophilus ducreyi strains were investigated with two monoclonal antibodies (MAbs), MAHD6 and MAHD7, raised against LOS from H. ducreyi ITM 2665. Closely related LOS, with defined structures, from Haemophilus influenzae, Bordetella pertussis, Aeromonas spp., and synthetic glycoproteins were also included in the analyses. The MAbs bound to conserved epitopes of LOS exposed on the surface of H. ducreyi. The MAb MAHD6 reacted with 8 of the 10 LOS from H. ducreyi but with none of the other Haemophilus or Bordetella spp. with structurally defined LOS. It is suggested that MAb MAHD6 binds to a LOS epitope (-DD-Hepp-1-->6-beta-D-Glcp-). This LOS epitope is not present in the hexasaccharide structure of LOS from H. ducreyi ITM 4747 (E. K. H. Schweda, A. C. Sundström, L. M. Eriksson, J. A. Jonasson, and A. A. Lindberg, J. Biol. Chem. 269:12040-12048, 1994). Because MAb MAHD6 reacts with the epitope mentioned above, it also discriminates between the two LOS structures, the hexasaccharide group and the nonasaccharide group, of H. ducreyi strains. MAb MAHD7 recognizes the common conserved inner core region of the LOS because it reacts with all H. ducreyi strains and with LOS with minor components in the inner core epitope structure. Rabbit polyclonal sera raised against the LOS from strains CCUG 4438 and CCUG 7470 were tested with the 10 LOS from the H. ducreyi strains. The antiserum to CCUG 7470 reacted with all H. ducreyi strains as did MAb MAHD7, whereas the antiserum to CCUG 4438 reacted with only its homologous strain and strain ITM 4747. Also, the LOSs of our reference strains CCUG 4438 and CCUG 7470 were structurally analyzed by use of sugar analyses and electrospray ionization-mass spectrometry. The hexasaccharide and nonasaccharide structures obtained from LOS of strains CCUG 4438 and CCUG 7470 were identical to the described LOS structures from H. ducreyi ITM 4747 and ITM 2665, respectively. In conclusion, the MAb MAHD6 recognizes an epitope present in the nonasaccharide LOS group, whereas the MAb MAHD7 recognizes a conserved epitope on LOS of H. ducreyi, which is present in all strains of H. ducreyi tested. Two major groups of oligosaccharides were distinguished by their LOS structures and the reactivity of monoclonal as well as polyclonal antibodies. The majority of H. ducreyi strains possess a nonasaccharide structure of LOS.

Ahmed, H J; Frisk, A; Mansson, J E; Schweda, E K; Lagergard, T

1997-01-01

327

A Fingerprint Recognizer using Fuzzy Evolutionary Programming  

Microsoft Academic Search

A fingerprint recognizing system is built with two principal components: the fingerprint administrator and the fingerprint recognizer. Fingerprints are identified by their special features such as ridge endings, ridge bifurcation, short ridges, and ridge enclosures, which are collectively called the minutiae. The fingerprint administrator uses the method of gray scale ridge tracing backed up by a validating procedure to extract

Tu Van Le; Ka Yeung Cheung; Minh Ha Nguyen

2001-01-01

328

The Developmental Dimensions of Recognizing Racist Thoughts  

ERIC Educational Resources Information Center

|This study focuses on understanding the developmental process that occurs when racist ideas are recognized as a part of college students' thought processes. Longitudinal data were collected from 29 Latino/a college students in order to illustrate how these students made meaning of racist thoughts when they began to recognize it. The framework of…

Torres, Vasti

2009-01-01

329

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

330

Conserving biodiversity by conserving land  

Microsoft Academic Search

Society faces difficult choices over whether to allow habitat conversion for economic gain versus conserving habitat to protect biodiversity. Because the conservation of biodiversity and the material well being of the human population are both important goals, it is important to set conservation priorities intelligently and minimize the reduction in other goals from pursuing conservation. In this paper, our objective

Stephen Polasky; Christian A. Vossler

2002-01-01

331

Hepatocyte Nuclear Factor 1 Regulates the Expression of the Organic Cation Transporter 1 via Binding to an Evolutionary Conserved Region in Intron 1 of the OCT1 Gene.  

PubMed

The organic cation transporter 1 (OCT1), also known as solute carrier family 22 member 1, is strongly and specifically expressed in the human liver. Here we show that the hepatocyte nuclear factor 1 (HNF1) regulates OCT1 transcription and contributes to the strong, liver-specific expression of OCT1. Bioinformatic analyses revealed strong conservation of HNF1 binding motifs in an evolutionary conserved region (ECR) in intron 1 of the OCT1 gene. Electrophoretic mobility shift and chromatin immunoprecipitation assays confirmed the specific binding of HNF1 to the intron 1 ECR. In reporter gene assays performed in HepG2 cells, the intron 1 ECR increased SV40 promoter activity by 22-fold and OCT1 promoter activity by 13-fold. The increase was reversed when the HNF1 binding sites in the intron 1 ECR were mutated or the endogenous HNF1? expression was downregulated with small interfering RNA. Following HNF1? overexpression in Huh7 cells, the intron 1 ECR increased SV40 promoter activity by 11-fold and OCT1 promoter activity by 6-fold. Without HNF1? overexpression, the increases were only 3- and 2-fold, respectively. Finally, in human liver samples, high HNF1 expression was significantly correlated with high OCT1 expression (r = 0.48, P = 0.002, n = 40). In conclusion, HNF1 is a strong regulator of OCT1 expression. It remains to be determined whether genetic variants, disease conditions, or drugs that affect HNF1 activity may affect the pharmacokinetics and efficacy of OCT1-transported drugs such as morphine, tropisetron, ondansetron, tramadol, and metformin. Beyond OCT1, this study demonstrates the validity and usefulness of interspecies comparisons in the discovery of functionally relevant genomic sequences. PMID:23922447

O'Brien, Valerie P; Bokelmann, Kristin; Ramírez, Jacqueline; Jobst, Karoline; Ratain, Mark J; Brockmöller, Jürgen; Tzvetkov, Mladen V

2013-08-06

332

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

333

Substrate Specificity-Conferring Regions of the Nonribosomal Peptide Synthetase Adenylation Domains Involved in Albicidin Pathotoxin Biosynthesis Are Highly Conserved within the Species Xanthomonas albilineans?  

PubMed Central

Albicidin is a pathotoxin produced by Xanthomonas albilineans, a xylem-invading pathogen that causes leaf scald disease of sugarcane. Albicidin is synthesized by a nonribosomal pathway via modular polyketide synthase and nonribosomal peptide synthetase (NRPS) megasynthases, and NRPS adenylation (A) domains are responsible for the recognition and activation of specific amino acid substrates. DNA fragments (0.5 kb) encoding the regions responsible for the substrate specificities of six albicidin NRPS A domains from 16 strains of X. albilineans representing the known diversity of this pathogen were amplified and sequenced. Polymorphism analysis of these DNA fragments at different levels (DNA, protein, and NRPS signature) showed that these pathogenicity loci were highly conserved. The conservation of these loci most likely reflects purifying selective pressure, as revealed by a comparison with the variability of nucleotide and amino acid sequences of two housekeeping genes (atpD and efp) of X. albilineans. Nevertheless, the 16 strains of X. albilineans were differentiated into several groups by a phylogenetic analysis of the nucleotide sequences corresponding to the NRPS A domains. One of these groups was representative of the genetic diversity previously found within the pathogen by random fragment length polymorphism and amplified fragment length polymorphism analyses. This group, which differed by three single synonymous nucleotide mutations, contained only four strains of X. albilineans that were all involved in outbreaks of sugarcane leaf scald. The amount of albicidin produced in vitro in agar and liquid media varied among the 16 strains of X. albilineans. However, no relationship among the amount of albicidin produced in vitro and the pathotypes and genetic diversity of the pathogen was found. The NRPS loci contributing to the synthesis of the primary structure of albicidin apparently are not involved in the observed pathogenicity differences among strains of X. albilineans.

Renier, Adeline; Vivien, Eric; Cociancich, Stephane; Letourmy, Philippe; Perrier, Xavier; Rott, Philippe C.; Royer, Monique

2007-01-01

334

Invariant natural killer T cells recognize glycolipids from pathogenic Gram-positive bacteria.  

PubMed

Natural killer T cells (NKT cells) recognize glycolipid antigens presented by CD1d. These cells express an evolutionarily conserved, invariant T cell antigen receptor (TCR), but the forces that drive TCR conservation have remained uncertain. Here we show that NKT cells recognized diacylglycerol-containing glycolipids from Streptococcus pneumoniae, the leading cause of community-acquired pneumonia, and group B Streptococcus, which causes neonatal sepsis and meningitis. Furthermore, CD1d-dependent responses by NKT cells were required for activation and host protection. The glycolipid response was dependent on vaccenic acid, which is present in low concentrations in mammalian cells. Our results show how microbial lipids position the sugar for recognition by the invariant TCR and, most notably, extend the range of microbes recognized by this conserved TCR to several clinically important bacteria. PMID:21892173

Kinjo, Yuki; Illarionov, Petr; Vela, José Luis; Pei, Bo; Girardi, Enrico; Li, Xiangming; Li, Yali; Imamura, Masakazu; Kaneko, Yukihiro; Okawara, Akiko; Miyazaki, Yoshitsugu; Gómez-Velasco, Anaximandro; Rogers, Paul; Dahesh, Samira; Uchiyama, Satoshi; Khurana, Archana; Kawahara, Kazuyoshi; Yesilkaya, Hasan; Andrew, Peter W; Wong, Chi-Huey; Kawakami, Kazuyoshi; Nizet, Victor; Besra, Gurdyal S; Tsuji, Moriya; Zajonc, Dirk M; Kronenberg, Mitchell

2011-09-04

335

Local Responses to Participatory Conservation in Annapurna Conservation Area, Nepal  

Microsoft Academic Search

Biodiversity conservation has undergone a profound change in philosophy, policies and management approaches over the last\\u000a forty years. The traditional top–down approach to nature protection has been widely criticized for failing to include critical\\u000a social elements in management practices, and is being gradually replaced by a slew of participatory strategies under the rubric\\u000a of bottom-up conservation. The new approach recognizes

Damodar Khadka

2010-01-01

336

A model assessing the conservation threats to freshwater turtles of Sub-Saharan Africa predicts urgent need for continental conservation planning  

Microsoft Academic Search

Global assessment of conservation threats to several taxonomic groups are urgently needed for species living in regions of\\u000a the world where field research is curtailed by logistic or economic constraints. For instance, it is now widely recognized\\u000a that freshwater turtles represent one of the most endangered groups of vertebrates in the world. This situation has been particularly\\u000a evident with Asian

Luca Luiselli

2009-01-01

337

I can't recognize your face but I can recognize its movement  

Microsoft Academic Search

Idiosyncratic facial movements can provide a route to facial identity (review in Roark, Barrett, Spence, Abdi, & O'Toole, 2003). However, it is unclear whether recognizing a face in this way involves the same cognitive or neural mechanisms that are involved in recognizing a static face. Three studies on a developmental prosopagnosic (C.S.) showed that although he is impaired at recognizing

Leslie L. Steede; Jeremy J. Tree; Graham J. Hole

2007-01-01

338

Learning to Recognize Patterns Without a Teacher.  

National Technical Information Service (NTIS)

The techniques of decision theory are applied to the problem of constructing machines that improve their ability to recognize patterns by extracting pertinent information from a previously unclassified sequence of observations; such machines are said to l...

S. C. Fralick

1965-01-01

339

Recognizing and treating ADHD in adults.  

PubMed

Patients with attention deficit hyperactivity disorder (ADHD) commonly present in primary care settings. Because untreated adult ADHD can impair patients' quality of life, clinicians need to know how to recognize and treat this potentially lifelong disorder. PMID:24153094

Vashak, Amy; Taylor, Lloyd A

2013-11-01

340

Residues in three conserved regions of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase are required for quaternary structure  

SciTech Connect

To explore the role of individual residues in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, small subunits with single amino acid substitutions in three regions of relative sequence conservation were produced by directed mutagenesis of the rbcS gene from Anabaena 7120. These altered small subunits were cosythesized with large subunits (from an expressed Anabaena rbcL gene) in Escherichia coli. Mutants were analyzed for effects on quaternary structure and catalytic activity. Changing Glu-13S (numbering used is that of the spinach enzyme) to Val, Trp-67S to Arg, Pro-73S to His, or Tyr-98S to Asn prevented accumulation of stable holoenzyme. Interpretation of these results using a model for the three-dimensional structure of the spinach enzyme based on x-ray crystallographic data suggests that our small subunit mutants containing substitutions at positions 13S and 67S probably do not assemble because of mispairing or nonpairing of charged residues on the interfacing surfaces of the large and small subunits. The failure of small subunits substituted at positions 73S or 98S to assemble correctly may result from disruption of intersubunit or intrasubunit hydrophobic pockets, respectively.

Fitchen, J.H.; McIntosh, L. (Michigan State Univ., East Lansing (USA)); Knight, S.; Andersson, I.; Branden, C.I. (Uppsala Biomedical Center (Sweden))

1990-08-01

341

Insect mitochondrial genomics 2: The complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements.  

PubMed

Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16,004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families. PMID:16936790

Stewart, James Bruce; Beckenbach, Andrew T

2006-07-01

342

Analysis of the RNA chaperoning activity of the hepatitis C virus core protein on the conserved 3'X region of the viral genome.  

PubMed

The core protein of hepatitis c virus (HCV) is a structural protein with potent RNA chaperoning activities mediated by its hydrophilic N-terminal domain D1, which is thought to play a key role in HCV replication. To further characterize the core chaperoning properties, we studied the interactions between core D1 and the conserved HCV 3'X genomic region required for genome replication. To this end, we monitored the real-time annealing kinetics of native and mutated fluorescently labelled 16-nt palindromic sequence (DLS) and 27-nt Stem Loop II (SL2) from X with their respective complementary sequences. Core D1 and peptides consisting of the core basic domains were found to promote both annealing reactions and partly switch the loop-loop interaction pathway, which predominates in the absence of peptide, towards a pathway involving the stem termini. The chaperone properties of the core D1 peptides were found to be mediated through interaction of their basic clusters with the oligonucleotide phosphate groups, in line with the absence of high affinity site for core on HCV genomic RNA. The core ability to facilitate the interconversion between different RNA structures may explain how this protein regulates RNA structural transitions during HCV replication. PMID:22127859

Sharma, Kamal Kant; de Rocquigny, Hugues; Darlix, Jean Luc; Lavergne, Jean-Pierre; Pénin, François; Lessinger, Jean-Marc; Mély, Yves

2011-11-29

343

Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding.  

PubMed

Transcription factor Rho of Eschericia coli is a ring-shaped homohexameric protein that terminates transcripts by its action on nascent RNAs. To test the functional importance of the phylogenetically highly conserved residues of the Q-loop region, four mutant Rho proteins, S281A, K283A, T286A and D290A, were isolated and analyzed for their biochemical properties. All four proteins were very defective in terminating transcripts in vitro at the bacteriophage lambda tR1 terminator and had corresponding defects in ATP hydrolysis activated by lambda cro RNA. Although the four proteins were normal or near normal in their sensitivity to cleavage with H(2)O(2) in the presence of Fe-EDTA and in their ability to bind to lambda cro RNA and ATP, they were defective in RNA-specific, secondary site interactions. This was indicated by the lack of protection from cleavage at their Q-loops by oligo(C) in the presence of poly(dC), and their defects in ATP hydrolysis activated by oligo(C) in the presence of poly(dC). This evidence, together with the observations that cleavage of the Q-loop residues is protected specifically by RNA, suggests that the Q-loop makes interactions with RNA that are essential for activation of ATP hydrolysis and the termination of transcription. PMID:11743718

Wei, R R; Richardson, J P

2001-12-14

344

Amino acid alterations within a highly conserved region of the Rous sarcoma virus src gene product pp60src inactivate tyrosine protein kinase activity.  

PubMed Central

Bisulfite mutagenesis techniques have been used to introduce single-point mutations within a region of the Rous sarcoma virus src gene defined by a BglI restriction endonuclease cleavage site. The mutants of Rous sarcoma virus that are produced by these techniques encode src proteins which contain single amino acid changes within a highly conserved amino acid sequence encompassing residues 430 to 433. DNA from the mutants CHpm26 ( Ala430 to Val), CHpm9 ( Pro431 to Ser), CHpm6 ( Glu432 to Lys), and CHpm65 ( Ala433 to Thr) each failed to transform chicken cells upon transfection, whereas DNA from CHpm59 (a third base alteration in the codon for Glu432 ) readily transformed chicken cells. Analysis of immune complexes containing the altered src proteins indicates that these proteins have decreased tyrosine protein kinase activity in vitro. In vivo labeling of cells infected with the mutant virus revealed diminished levels of the tyrosine-phosphorylated 34,000-molecular-weight protein. These data indicate that mutations within the sequence Ala430 - Pro431 - Glu432 - Ala433 lead to alterations in pp60src-specific tyrosine protein kinase activity and a concomitant loss of transforming potential of the mutant virus. Images

Bryant, D L; Parsons, J T

1984-01-01

345

Systematic Analysis of the Amino Acid Residues of Human Papillomavirus Type 16 E7 Conserved Region 3 Involved in Dimerization and Transformation ?  

PubMed Central

The human papillomavirus (HPV) E7 oncoprotein exists as a dimer and acts by binding to many cellular factors, preventing or retargeting their function and thereby making the infected cell conducive for viral replication. Dimerization of E7 is attributed primarily to the C-terminal domain, referred to as conserved region 3 (CR3). CR3 is highly structured and is necessary for E7's transformation ability. It is also required for binding of numerous E7 cellular targets. To systematically analyze the molecular mechanisms by which HPV16 E7 CR3 contributes to carcinogenesis, we created a comprehensive panel of mutations in residues predicted to be exposed on the surface of CR3. We analyzed our novel collection of mutants, as well as mutants targeting predicted hydrophobic core residues of the dimer, for the ability to dimerize. The same set of mutants was also assessed functionally for transformation capability in a baby rat kidney cell assay in conjugation with activated ras. We show that some mutants of HPV16 E7 CR3 failed to dimerize yet were still able to transform baby rat kidney cells. Our results identify several novel E7 mutants that abrogate transformation and also indicate that E7 does not need to exist as a stable dimer in order to transform cells.

Todorovic, Biljana; Massimi, Paola; Hung, Katherine; Shaw, Gary S.; Banks, Lawrence; Mymryk, Joe S.

2011-01-01

346

Regulation of zinc-responsive Slc39a5 (Zip5) translation is mediated by conserved elements in the 3'-untranslated region.  

PubMed

Translation of the basolateral zinc transporter ZIP5 is repressed during zinc deficiency but Zip5 mRNA remains associated with polysomes and can be rapidly translated when zinc is repleted. Herein, we examined the mechanisms regulating translation of Zip5. The 3'-untranslated region (UTR) of Zip5 mRNA is well conserved among mammals and is predicted by mFOLD to form a very stable stem-loop structure. Three algorithms predict this structure to be flanked by repeated seed sites for miR-328 and miR-193a. RNAse footprinting supports the notion that a stable stem-loop structure exists in this 3'-UTR and electrophoretic mobility shift assays detect polysomal protein(s) binding specifically to the stem-loop structure in the Zip5 3'-UTR. miR-328 and miR-193a are expressed in tissues known to regulate Zip5 mRNA translation in response to zinc availability and both are polysome-associated consistent with Zip5 mRNA localization. Transient transfection assays using native and mutant Zip5 3'-UTRs cloned 3' to luciferase cDNA revealed that the miRNA seed sites and the stem-loop function together to augment translation of Zip5 mRNA when zinc is replete. PMID:22113231

Weaver, Benjamin P; Andrews, Glen K

2011-11-24

347

Alternative splicing within the elk-1 5' untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2.  

PubMed

The 5' untranslated region (UTR) plays a central role in the regulation of mammalian translation initiation. Key components include RNA structure, upstream AUGs (uAUGs), upstream open reading frames (uORFs), and internal ribosome entry site elements that can interact to modulate the readout. We previously reported the characterization of two alternatively spliced 5' UTR isoforms of the human elk-1 gene. Both contain two uAUGs and a stable RNA stem-loop, but the long form (5' UTR(L)) was more repressive than the short form (5' UTR(S)) for initiation at the ELK-1 AUG. We now demonstrate that ELK-1 expression arises by a combination of leaky scanning and reinitiation, with the latter mediated by the small uORF2 conserved in both spliced isoforms. In HEK293T cells, a considerable fraction of ribosomes scans beyond the ELK-1 AUG in a reinitiation mode. These are sequestered by a series of out-of-frame AUG codons that serve to prevent access to a second in-frame AUG start site used to express short ELK-1 (sELK-1), an N-terminally truncated form of ELK-1 that has been observed only in neuronal cells. We present evidence that all these events are fine-tuned by the nature of the 5' UTR and the activity of the ? subunit of eukaryotic initiation factor 2 and provide insights into the neuronal specificity of sELK-1 expression. PMID:22354998

Rahim, Gwendoline; Araud, Tanguy; Jaquier-Gubler, Pascale; Curran, Joseph

2012-02-21

348

Collections Conservation.  

ERIC Educational Resources Information Center

Collections conservation is an approach to the preservation treatment of books and book-like materials that is conceptualized and organized in terms of large groups of materials. This guide is intended to enable a library to evaluate its current collections conservation activities. The introduction describes collections conservation and gives…

DeCandido, Robert

349

Collections Conservation.  

ERIC Educational Resources Information Center

|Collections conservation is an approach to the preservation treatment of books and book-like materials that is conceptualized and organized in terms of large groups of materials. This guide is intended to enable a library to evaluate its current collections conservation activities. The introduction describes collections conservation and gives…

DeCandido, Robert

350

Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15 1 1 Edited by J. Karn  

Microsoft Academic Search

Ribosomal protein S15 recognizes a highly conserved target on 16 S rRNA, which consists of two distinct binding regions. Here, we used extensive site-directed mutagenesis on a Escherichia coli 16 S rRNA fragment containing the S15 binding site, to investigate the role of conserved nucleotides in protein recognition and to evaluate the relative contribution of the two sites. The effect

Alexander Serganov; Lionel Bénard; Claude Portier; Eric Ennifar; Maria Garber; Bernard Ehresmann; Chantal Ehresmann

2001-01-01

351

Phylogeographic study based on intraspecific sequence variation of chloroplast DNA for the conservation of genetic diversity in the Japanese endangered species Primula sieboldii  

Microsoft Academic Search

To gather information on intraspecific phylogeography for use in conservation programs for the endangered species Primula sieboldii in Japan, we analyzed sequence variation in five noncoding regions of chloroplast DNA. Twenty-two distinct haplotypes were recognized in total. The distribution of most haplotypes was geographically confined, but one haplotype was widely distributed throughout northern Japan, and several haplotypes were found in

M Honjo; S Ueno; Y Tsumura; I Washitani; R Ohsawa

2004-01-01

352

Identification of conserved regulatory elements in upstream promoter regions of mammals at relaxed thresholds by comparative genomics - a case study using PEPCK  

Technology Transfer Automated Retrieval System (TEKTRAN)

Background Comparative genomics is the primary method to discover regulatory elements by identifying conserved sequences due to evolutionary constraints by cross-species genome comparison. Except for the most conserved and prominent transcription factor binding sites (TFBS), there is a general lack ...

353

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

354

MSY2 and MSY4 Bind a Conserved Sequence in the 3? Untranslated Region of Protamine 1 mRNA In Vitro and In Vivo  

PubMed Central

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 UACCACAUCCACU (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.

Giorgini, Flaviano; Davies, Holly G.; Braun, Robert E.

2001-01-01

355

Analysis of the murine Hox-2.7 gene: conserved alternative transcripts with differential distributions in the nervous system and the potential for shared regulatory regions.  

PubMed Central

In this study we have investigated the organization and regulation of the mouse Hox-2.7 gene. There are several alternative transcripts some of which are conserved between mouse and humans. By Northern and in situ analysis we are able to identify at least three types of transcripts which are different in size and splicing pattern and have distinctly different boundaries of expression in the nervous system. One subset of the endogenous transcripts has a boundary of expression that corresponds to the adjacent Hox-2.8 gene instead of Hox-2.7. In another type of transcript there is an alternative reading frame which predicts a protein that has homology to an enzyme ATPase and suggests that a non-homeobox containing gene may be located in the Hox-2 cluster. A Hox-2.7-lacZ transgene is expressed in a similar pattern to the endogenous gene in that spatially-restricted domains of expression are seen in the branchial arches, neural tube, paraxial mesoderm (somites), cranial ganglia, neural crest and gut. However, the anterior boundaries of transgene expression only correspond to the subset of Hox-2.7 transcripts which map to the Hox-2.8 boundary. The proximity of a Hox-2.7 promoter to regions which regulate the adjacent Hox-2.6 gene and the expression of transgenic and endogenous transcripts in a Hox-2.8 pattern, suggest that regulatory elements may be shared by neighbouring genes to establish the complete expression pattern. Images

Sham, M H; Hunt, P; Nonchev, S; Papalopulu, N; Graham, A; Boncinelli, E; Krumlauf, R

1992-01-01

356

1,25(OH)2 vitamin D3 promotes FOXP3 expression via binding to vitamin D response elements in its conserved non-coding sequence region  

PubMed Central

Forkhead box P3 (FOXP3)-positive regulatory T cells (Treg) are a unique subset of T cells with immune regulatory properties. Treg cells can be induced from non-Treg CD4+ T cells (induced Treg, iTreg) by T cell receptor (TCR) triggering, IL-2 and TGF-? or retinoic acid. 1,25(OH)2 vitamin D3 (VD3) affects the functions of immune cells including T cells. 1,25(OH)2VD3 binds the nuclear vitamin D receptor (VDR) that binds target DNA sequences known as the vitamin D response element (VDRE). Although 1,25(OH)2VD3 can promote FOXP3 expression in CD4+ T cells with TCR triggering and IL-2, it is unknown whether this effect of 1,25(OH)2VD3 is mediated through direct binding of VDR to the FOXP3 gene without involving other molecules. Also, it is unclear whether FOXP3 expression in 1,25(OH)2VD3-induced Treg (VD-iTreg) cells is critical for the inhibitory function of these cells. Here we demonstrated the presence of VDREs in the intronic conserved non-coding sequence (CNS) region +1714 to +2554 of the human FOXP3 gene and the enhancement of the FOXP3 promoter activity by such VDREs in response to 1,25(OH)2VD3. In addition, VD-iTreg cells suppressed the proliferation of target CD4+ T cells and this activity was dependent on FOXP3 expression. These findings suggest that 1,25(OH)2VD3 can affect human immune responses by regulating FOXP3 expression in CD4+ T cells through direct VDR binding to the FOXP3 gene which is essential for inhibitory function of VD-iTreg cells.

Kang, Seong Wook; Kim, Sang Hyun; Lee, Naeun; Lee, Won-Woo; Hwang, Kyung-A; Shin, Min Sun; Lee, Seung-Hyun; Kim, Wan-Uk; Kang, Insoo

2012-01-01

357

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

358

Conservation Laws  

NASA Astrophysics Data System (ADS)

In the case of the free particle, we interpreted various components of the energy-momentum-stress density as fluxes of energy and momentum. This interpretation can obviously be extended also to particle ensembles and gases. When we speak of fluxes we usually think of quantities that are conserved. In special relativity, energy and momentum are conserved. In general relativity, they are no longer generally conserved, at least if we do not include the energy and momentum of the gravitational field itself. Nevertheless, their densities and fluxes satisfy a covariant generalization of a true conservation law, which is quite easy to obtain.

Dewitt, Bryce; Christensen, Steven M.

359

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

360

Recognizing and Responding to a Suicide Crisis.  

ERIC Educational Resources Information Center

|Data from therapists who were treating 26 patients when they committed suicide were utilized to identify warning signs. Problems in communication between patient and therapist were identified as factors interfering with crisis recognition. Evaluation of the identified affects and behaviors may help therapists recognize a suicide crisis. (BF)|

Hendin, Herbert; Maltsberger, John T.; Lipschitz, Alan; Haas, Ann Pollinger; Kyle, Jennifer

2001-01-01

361

Recognizing User Context via Wearable Sensors  

Microsoft Academic Search

We describe experiments in recognizing a person's situation from only a wearable camera and microphone. The types of situations considered in these experiments are coarse locations (such as at work, in a subway or in a grocery store) and coarse events (such as in a conversation or walking down a busy street) that would require only global, non-attentional features to

Brian P. Clarkson; Kenji Mase; Alex Pentland

2000-01-01

362

Training agents to recognize text by example  

Microsoft Academic Search

An important function of an agent is to be "on the lookout" forbits of information that are interesting to its user, even if theseitems appear in the midst of a larger body of unstructuredinformation. But how to tell these agents which patterns aremeaningful and what to do with the result?Especially when agents are used to recognize text, they areusually driven

Henry Lieberman; Bonnie A. Nardi; David J. Wright

1999-01-01

363

Towards a Learning Companion that Recognizes Affect  

Microsoft Academic Search

This paper reports work in progress to build a Learning Companion, a computerized system sensitive to the affective aspects of learning, which facilitates the child's own efforts at learning. Learning related to science, math, engineering, and technology naturally involves failure and a host of associated affective responses. This article describes techniques and tools being developed to recognize affective states important

Ashish Kapoor; Selene Mota; Rosalind W. Picard

2001-01-01

364

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

365

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

366

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

367

Recognizing self in puppet controlled virtual avatars  

Microsoft Academic Search

Recent work in neuroscience suggests that there is a common coding in the brain between perception, imagination and execution of movement. Further, this common coding is considered to allow people to recognize their own movements when presented as abstract representations, and coordinate with these movements better. We are investigating how this 'own movement effect' could be extended to improve the

Ali Mazalek; Michael Nitsche; Sanjay Chandrasekharan; Tim Welsh; Paul Clifton; Andrew Quitmeyer; Firaz Peer; Friedrich Kirschner

2010-01-01

368

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

369

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

370

RECOGNIZING MANTLE PLUMES IN THE GEOLOGICAL RECORD  

Microsoft Academic Search

? Abstract Mantle plumes are recognized by domal uplift, triple junction rift- ing, and especially the presence of a large igneous province (LIP), dominated in the Phanerozoic by flood basalts, and in the Proterozoic by the exposed plumbing system of dykes, sills, and layered intrusions. In the Archean, greenstone belts that contain komatiites have been linked to plumes. In addition,

Richard E. Ernst; Kenneth L. Buchan

2003-01-01

371

License Processing: Recognizing Characters in License Plates  

Microsoft Academic Search

This paper describes an approach to character recognition which is designed to recognize Lebanese license plate characters by extracting lines of information from vehicle photographs. The algorithm is designed to extract signatures at strategic positions on the character, then studies the information taken from the hotspots and identifies the different characters. The algorithm is simple and fast however its simplicity

Hasan R. Obeid; Rached N. Zantout

2007-01-01

372

Reading Programs in Nationally Recognized Elementary Schools.  

ERIC Educational Resources Information Center

Analyzes self-reports and site visitor reports of 300 of the nationally recognized "Blue Ribbon" elementary schools representing 1985-86, 1987-88, 1989-90, and 1991-92 recognition years. Finds that more schools were using literature-based instruction, grouping flexibly, using computer-assisted instruction, providing in-class remedial instruction,…

Kletzien, Sharon Benge

1996-01-01

373

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

374

The tetrasaccharide L-alpha-D-heptose1-->2-L-alpha-D-heptose1--> 3-L-alpha-D-heptose1-->(3-deoxy-D-manno-octulosonic acid) and phosphate in lipid A define the conserved epitope in Haemophilus lipopolysaccharides recognized by a monoclonal antibody.  

PubMed Central

A murine monoclonal antibody, MAHI 3 (immunoglobulin G2b), that is broadly reactive with Haemophilus influenzae lipopolysaccharides (LPSs) but nonreactive with all enterobacterial LPSs tested was generated by fusing mouse myeloma cells with spleen cells of BALB/c mice immunized with azide-killed H. influenzae RM.7004. MAHI 3 bound to all H. influenzae, all other human Haemophilus spp., all Bordetella pertussis and Bordetella parapertussis, and all Aeromonas spp. tested but not to any Neisseria or Moraxella catarrhalis strains, as determined by enzyme immunoassay, colony dot immunoblotting, and immunoblotting. In an inhibition enzyme immunoassay, MAHI 3 reacted with all 45 H. influenzae LPSs tested but not with the LPS from the rough mutant I69 Rd-/b+, which has only 3-deoxy-D-manno-octulosonic acid (P) [Kdo(P)] and lipid A. The antibody was not inhibited by H. influenzae lipid A or lipid-free polysaccharide isolated after mild acid hydrolysis. Only native LPSs show positive inhibitory activity, indicating that part of lipid A is involved in the binding of MAHI 3. From the results, it is indicated that the structural element recognized by MAHI 3 is Hep alpha 1-->2Hep alpha 1-->3Hep alpha 1-->Kdo together with part of lipid A, including the phosphate.

Borrelli, S; Hegedus, O; Shaw, D H; Jansson, P E; Lindberg, A A

1995-01-01

375

Conserved regions of the Plasmodium falciparum rhoptry-associated protein 3 mediate specific host-pathogen interactions during invasion of red blood cells  

Microsoft Academic Search

Invasion of red blood cells (RBCs) by the Plasmodium falciparum malaria merozoite is mediated by parasite surface molecules and proteins contained within apical organelles that are capable of recognizing receptors on the membrane of RBCs. The identification and characterization of these P. falciparum invasion-associated proteins is the first step for unveiling potential new drug and vaccine target molecules to eradicate

Jeison García; Hernando Curtidor; Magnolia Vanegas; Gabriela Arévalo-Pinzon; Manuel A. Patarroyo; Manuel E. Patarroyo

2010-01-01

376

Recognizing and Responding to Student Affect  

Microsoft Academic Search

This paper describes the use of wireless sensors to recognize student emotion and the use of pedagogical agents to respond\\u000a to students with these emotions. Minimally invasive sensor technology has reached such a maturity level that students engaged\\u000a in classroom work can us sensors while using a computer-based tutor. The sensors, located on each of 25 student’s chair, mouse,\\u000a monitor,

Beverly Park Woolf; Toby Dragon; Ivon Arroyo; David G. Cooper; Winslow Burleson; Kasia Muldner

2009-01-01

377

Data sampling for improved speech recognizer training  

Microsoft Academic Search

Proper data selection for training a speech recognizer can be im-portant for reducing costs of developing systems on new tasks and exploratory experiments, but it is also useful for efficient leveraging of the increasingly large speech resources available for training large vocabulary systems. In this work, we investi-gate various sampling methods, comparing the likelihood crite-rion to new acoustic measures motivated

Takahiro Shinozaki; Mari Ostendorf; Les E. Atlas

2005-01-01

378

Polymorphisms of MICA recognized by human alloantibodies  

Microsoft Academic Search

MICA antigens are polymorphic glycoproteins expressed on the surface of human endothelial cells and other cells. Antibodies\\u000a against MICA have been found in transplant recipients and were found to be associated with decreased survival of kidney allografts.\\u000a In the present work, we investigated the polymorphisms that are recognized by antibodies against MICA. Soluble MICA recombinant\\u000a proteins representing 11 common alleles,

Yizhou Zou; Zhiqiang Qin; Allison Silveus; Yisun Fan; Peter Stastny

2009-01-01

379

Recognizing Human Actions by Their Pose  

Microsoft Academic Search

The topic of human action recognition from image sequences gained increasing interest throughout the last years. Interestingly,\\u000a the majority of approaches are restricted to dynamic motion features and therefore not universally applicable. In this paper,\\u000a we propose to recognize human actions by evaluating a distribution over a set of predefined static poses which we refer to\\u000a as pose primitives. We

Christian Thurau; Václav Hlavá?

380

PRECISION CONSERVATION  

Technology Transfer Automated Retrieval System (TEKTRAN)

Precision conservation utilizes a set of technologies and procedures that link mapped variables with analytical capabilities to appropriate management actions. It requires the integration of spatial technologies of global positioning systems, remote sensing and geographic information systems with t...

381

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

382

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

383

Energy Conservation  

ERIC Educational Resources Information Center

Comments on The Potential for Energy Conservation,'' a study by the Office of Emergency Preparedness, emphasizing the coming dependence on foreign oil, and presses for government influence to encourage development of more efficient cars. (AL)

Abelson, Philip H.

1972-01-01

384

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.

385

Leadership: a new frontier in conservation science.  

PubMed

Leadership is a critical tool for expanding the influence of conservation science, but recent advances in leadership concepts and practice remain underutilized by conservation scientists. Furthermore, an explicit conceptual foundation and definition of leadership in conservation science are not available in the literature. Here we drew on our diverse leadership experiences, our reading of leadership literature, and discussions with selected conservation science leaders to define conservation-science leadership, summarize an exploratory set of leadership principles that are applicable to conservation science, and recommend actions to expand leadership capacity among conservation scientists and practitioners. We define 2 types of conservation-science leadership: shaping conservation science through path-breaking research, and advancing the integration of conservation science into policy, management, and society at large. We focused on the second, integrative type of leadership because we believe it presents the greatest opportunity for improving conservation effectiveness. We identified 8 leadership principles derived mainly from the "adaptive leadership" literature: recognize the social dimension of the problem; cycle frequently through action and reflection; get and maintain attention; combine strengths of multiple leaders; extend your reach through networks of relationships; strategically time your effort; nurture productive conflict; and cultivate diversity. Conservation scientists and practitioners should strive to develop themselves as leaders, and the Society for Conservation Biology, conservation organizations, and academia should support this effort through professional development, mentoring, teaching, and research. PMID:19183215

Manolis, Jim C; Chan, Kai M; Finkelstein, Myra E; Stephens, Scott; Nelson, Cara R; Grant, Jacqualine B; Dombeck, Michael P

2009-01-13

386

40 CFR 745.88 - Recognized test kits.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 false Recognized test kits. 745.88 Section 745.88 Protection...Renovation § 745.88 Recognized test kits. (a) Effective June 23, 2008, EPA recognizes the test kits that have been determined by...

2013-07-01

387

40 CFR 745.88 - Recognized test kits.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Recognized test kits. 745.88 Section 745.88 Protection...Renovation § 745.88 Recognized test kits. (a) Effective June 23, 2008, EPA recognizes the test kits that have been determined by...

2010-07-01

388

40 CFR 745.88 - Recognized test kits.  

Code of Federal Regulations, 2010 CFR

...2009-07-01 false Recognized test kits. 745.88 Section 745.88 Protection...Renovation § 745.88 Recognized test kits. (a) Effective June 23, 2008, EPA recognizes the test kits that have been determined by...

2009-07-01

389

Biogeography and conservation of taxa from remote regions: An application of ecological-niche based models and GIS to North-African canids  

Microsoft Academic Search

In North Africa, and especially in the Sahara Desert, biodiversity is poorly known. Of the five widespread canid species present, one is Data Deficient, three are considered widespread although habitat selection could limit their area of occupancy, and distribution maps available are coarse for conservation planning. This study identifies biogeographic patterns in North-African canids through the combination of high resolution

José C. Brito; André L. Acosta; Francisco Álvares; Fabrice Cuzin

2009-01-01

390

Detection of erythromycin resistance by the polymerase chain reaction using primers in conserved regions of erm rRNA methylase genes.  

PubMed Central

Genes belonging to different erm DNA hybridization classes were selectively amplified by polymerase chain reaction with a pair of oligonucleotides that corresponded to conserved amino acid motifs in known ERM methylases. Identification of the resistance mechanism was possible despite substantial nucleotide sequence diversity among the erythromycin resistance genes.

Arthur, M; Molinas, C; Mabilat, C; Courvalin, P

1990-01-01

391

Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions  

PubMed Central

Modular domains mediating specific protein–protein interactions play central roles in the formation of complex regulatory networks to execute various cellular activities. Here we identify a novel domain PB1 in the budding yeast protein Bem1p, which functions in polarity establishment, and mammalian p67phox, which activates the microbicidal phagocyte NADPH oxidase. Each of these specifically recognizes an evolutionarily conserved PC motif to interact directly with Cdc24p (an essential protein for cell polarization) and p40phox (a component of the signaling complex for the oxidase), respectively. Swapping the PB1 domain of Bem1p with that of p67phox, which abolishes its interaction with Cdc24p, confers on cells temperature- sensitive growth and a bilateral mating defect. These phenotypes are suppressed by a mutant Cdc24p harboring the PC motif-containing region of p40phox, which restores the interaction with the altered Bem1p. This domain-swapping experiment demonstrates that Bem1p function requires interaction with Cdc24p, in which the PB1 domain and the PC motif participate as responsible modules.

Ito, Takashi; Matsui, Yasushi; Ago, Tetsuro; Ota, Kazuhisa; Sumimoto, Hideki

2001-01-01

392

Conservation and sustainable exploitation of mangroves in Hong Kong  

Microsoft Academic Search

Mangroves are important wetlands along tropical and subtropical coasts that have been seriously damaged due to excessive exploitation. The need to conserve mangroves has been recognized since the 1970s. The degree of mangrove conservation ranges from rigid ecological conservation (for \\

Nora F. Y. Tam; Y. S. Wong

2002-01-01

393

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

2008-05-06

394

Proctalgia fugax: would you recognize it?  

PubMed

Proctalgia fugax is characterized by sudden and sometimes severe rectal pain that occurs by day or night at irregular intervals. The pain results from dysfunction of the internal anal sphincter. Proctalgia fugax has a uniform clinical picture, and it can be easily diagnosed when recognized. The patient can be assured that nothing serious is wrong. Expensive tests, such as computed tomography or magnetic resonance imaging of the pelvis, are not required. Treatment may be difficult, but if the attacks of pain are numerous and severe,, a calcium channel blocker such as nifedipine (Adalat, Procardia) should be tried. PMID:8604412

Babb, R R

1996-04-01

395

Home hazards: can children recognize the dangers?  

PubMed

To have effective injury prevention programs for children, solid education must be provided. Initially, the parental responsibility includes protecting and instructing the child about dangerous situations. However, when children can recognize a hazard for themselves, this becomes the basis for behavior change according to the health belief model. For trauma centers providing injury prevention services, knowing what a child perceives as a safety issue can be instrumental in correctly targeting curriculum. The following is a compilation of responses of 90 children who participated in a 2008 Home Hazard Recognition Station at a local Safe Kids event. PMID:18820562

Schooley, Carolyn B; Kelly, Amanda R

396

Recognizing women in the archaeological record  

SciTech Connect

Primary sexual characteristics are usually absent in the archaeological record. The recovered secondary sex markers in bone morphology or mortuary context reflect the lifelong integrated biocultural experience of the individual man or woman. Internal patterns of variability within and between sexes can be recognized but are too frequently masked by traditional descriptive and univariate analyses. Fortunately, a more detailed picture of life experience is gained by analyzing chemical composition (isotopic and elemental) of hard tissues using an analytical anthropology approach and by examining the variation in novel ways. 7 figs.

Bumsted, M.P.

1987-01-01

397

Fibromyalgia: recognizing and treating an elusive syndrome.  

PubMed

The noninflammatory, diffuse pain syndrome recognized as fibromyalgia primarily affects women between puberty and menopause. Symptoms, in addition to musculoskeletal pain and tender points, can include fatigue, nonrestorative sleep, and depression. A precipitating event such as abrupt cessation of exercise, physical injury, or prior debilitating illness can often be identified. Aerobic exercise is usually protective, but sporadic training patterns or other precipitants can place even well-trained athletes at risk. Patients need to know that they can alter the course of this syndrome. Treatment should include attempts to reverse the precipitating event, plus education, aerobic exercise, correction of any sleep disturbance, analgesia, and physical therapy. PMID:20086803

Gremillion, R B

1998-04-01

398

Conservation of glp-1 regulation and function in nematodes.  

PubMed Central

The Caenorhabditis elegans (Ce) glp-1 gene encodes a Notch-like receptor. We have cloned glp-1 from C. briggsae (Cb) and C. remanei (Cr), two Caenorhabditis species that have diverged from C. elegans by roughly 20-40 million years. By sequence analysis, we find that the Cb-GLP-1 and Cr-GLP-1 proteins have retained the same motif architecture as Ce-GLP-1, including number of domains. In addition, two regions (CC-linker and regions flanking the ANK repeats) are as highly conserved as regions previously recognized as essential for signaling (e.g., ANK repeats). Phylogenetic analysis of glp-1 sequences suggests a C. briggsae/C. remanei clade with C. elegans as a sister taxon. Using RNAi to test biological functions, we find that Ce-glp-1, Cb-glp-1, and Cr-glp-1 are all required for proliferation of germline stem cells and for specifying blastomere fates in the embryo. In addition, certain biological roles of Cb-glp-1, e.g., in the vulva, have diverged from those of Ce-glp-1 and Cr-glp-1, suggesting a change in either regulation or function of the Cb-glp-1 gene during evolution. Finally, the regulation of glp-1 mRNA, previously analyzed for Ce-glp-1, is conserved in Cb-glp-1, and we identify conserved 3' UTR sequences that may serve as regulatory elements.

Rudel, D; Kimble, J

2001-01-01

399

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

400

Ants recognize foes and not friends.  

PubMed

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. PMID:19364750

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

2009-04-01

401

Use of crop residue and manure to conserve water and enhance nutrient availability and pearl millet yields in an arid tropical region  

Microsoft Academic Search

Crop residues and manures are often used in temperate regions to control soil erosion and maintain soil organic matter. Because crop residues and manures oxidize more rapidly in warmer climates, benefits from use of these materials may not be as evident for tropical as for temperate region agriculture, especially in drier regions where residues are limited. In 1991 and 1992,

R. K. Aggarwal; Praveen-Kumar; J. F. Power

1997-01-01

402

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae  

Microsoft Academic Search

BACKGROUND: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications: a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c)

Davide Rambaldi; Alessandro Guffanti; Paolo Morandi; Giuseppe Cassata

2005-01-01

403

Investigating the potential of conserved inner core oligosaccharide regions of Moraxella catarrhalis lipopolysaccharide as vaccine antigens: accessibility and functional activity of monoclonal antibodies and glycoconjugate derived sera  

Microsoft Academic Search

We investigated the conservation and antibody accessibility of inner core epitopes of Moraxella catarrhalis lipopolysaccharide (LPS) in order to assess their potential as vaccine candidates. Two LPS mutants, a single mutant designated\\u000a lgt2 and a double mutant termed lgt2\\/lgt4, elaborating truncated inner core structures were generated in order to preclude expression of host-like outer core structures\\u000a and to create an

Andrew D. Cox; Frank St. Michael; Chantelle M. Cairns; Suzanne Lacelle; Amy Lea Filion; Dhamodharan Neelamegan; Cory Q. Wenzel; Heather Horan; James C. Richards

2011-01-01

404

Accessibility and conservation  

PubMed Central

Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. We determined features that discriminate functional from non-functional interactions and assessed the influence of these features on genome-wide target predictions. For this purpose, we compiled a set of 71 experimentally verified sRNA–target pairs from Escherichia coli and Salmonella enterica. Furthermore, we collected full-length 5? untranslated regions by using genome-wide experimentally verified transcription start sites.   Only interaction sites in sRNAs, but not in targets, show significant sequence conservation. In addition to this observation, we found that the base pairing between sRNAs and their targets is not conserved in general across more distantly related species. A closer inspection of RybB and RyhB sRNAs and their targets revealed that the base pairing complementarity is only conserved in a small subset of the targets. In contrast to conservation, accessibility of functional interaction sites is significantly higher in both sRNAs and targets in comparison to non-functional sites. Based on the above observations, we successfully used the following constraints to improve the specificity of genome-wide target predictions: the region of interaction initiation must be located in (1) highly accessible regions in both interaction partners or (2) unstructured conserved sRNA regions derived from reliability profiles of multiple sRNA alignments. Aligned sequences of homologous sRNAs, functional and non-functional targets, and a sup document with sup tables, figures and references are available at www.bioinf.uni-freiburg.de/Supplements/srna-interact-feat/.

Richter, Andreas S.; Backofen, Rolf

2012-01-01

405

Water Conservation  

NSDL National Science Digital Library

In this lesson, students study the availability of water on Earth and discuss methods that can be used to purify and conserve this critical resource. Using multimedia interactives, video, and classroom activities, they will identify sources of fresh water available for consumption, understand the need for water conservation, and compare the benefits and drawbacks of different water management techniques. They will also assess how much water they and their families typically use, and think about ways to reduce their water usage. Finally, students explore different techniques being employed for water management around the world, including the use of dams to create reservoirs.

2005-01-01

406

Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity  

Microsoft Academic Search

Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant\\u000a target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely\\u000a unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat\\u000a NKR-P1A and NKR-P1B, mouse

Žofie Sovová; Vladimír Kopecký; Tomáš Pazderka; Kate?ina Hofbauerová; Daniel Rozbeský; Ond?ej Van?k; Karel Bezouška; Rüdiger Ettrich

2011-01-01

407

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

408

Recognizing MSTAR target variants and articulations  

NASA Astrophysics Data System (ADS)

The focus of this paper is recognizing articulated vehicles and actual vehicle configuration variants in real SAR images from the MSTAR public data. Using SAR scattering center locations and magnitudes as features, the invariance of these features is shown with articulation (i.e. turret rotation for the T72 tank and ZSU 23/4 gun), with configuration variants and with a small change in depression angle. This scatterer location and magnitude quasi-invariance (e.g. location within one pixel, magnitude within about ten percent in radar cross- section) is used as a basis for development of a SAR recognition engine that successfully identified real articulated and non-standard configuration vehicles based on non-articulated, standard recognition models. Identification performance results are presented as vote space scatter plots and ROC curves for configuration variants, for articulated objects and for a small change in depression angle with the MSTAR data.

Bhanu, Bir; Jones, Grinnell

1999-08-01

409

Position, rotation, and intensity invariant recognizing method  

DOEpatents

A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output The U.S. Government has rights in this invention pursuant to Contract No. DE-AC04-76DP00789 between the U.S. Department of Energy and AT&T Technologies, Inc.

Ochoa, Ellen (Pleasanton, CA); Schils, George F. (San Ramon, CA); Sweeney, Donald W. (Alamo, CA)

1989-01-01

410

Neural nets for radio Morse code recognizing  

NASA Astrophysics Data System (ADS)

This paper proposes a neural network recognition system for hand keying Radio Morse codes. The system has been trained and tested on real world data recorded from amateur radio Morse codes. The overall recognizing process can be partitioned into 3 major parts, the preprocessing, the feature extracting, and the character decoding. The whole operation is able to be performed in real-time on a PC/486 system. Self-Organizing Maps are used intensively in the recognition system to adaptively learn the variation of the Morse code signal. The average performance of the recognition system has been achieved about 96.4% with a rejection rate of 6.5%. It is hoped that many of the techniques would be applicable to a wide range of DSP and recognition tasks.

Fu, Hsin-Chia; Lin, Y. Y.; Pao, Hsiao-Tien

1993-09-01

411

Recognizing familial myeloid leukemia in adults.  

PubMed

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. PMID:23926458

Nickels, Eric M; Soodalter, Jesse; Churpek, Jane E; Godley, Lucy A

2013-08-01

412

Chaotic itinerancy in coupled dynamical recognizers  

NASA Astrophysics Data System (ADS)

We argue that chaotic itinerancy in interaction between humans originates in the fluctuation of predictions provided by the nonconvergent nature of learning dynamics. A simple simulation model called the coupled dynamical recognizer is proposed to study this phenomenon. Daily cognitive phenomena provide many examples of chaotic itinerancy, such as turn taking in conversation. It is therefore an interesting problem to bridge two chaotic itinerant phenomena. A clue to solving this is the fluctuation of prediction, which can be translated as ``hot prediction'' in the context of cognitive theory. Hot prediction is simply defined as a prediction based on an unstable model. If this approach is correct, the present simulation will reveal some dynamic characteristics of cognitive interactions.

Ikegami, Takashi; Morimoto, Gentaro

2003-09-01

413

EPA recognizes industry leaders for beneficial use  

SciTech Connect

The EPA's Coal Combustion Products Partnership C{sup 2}P{sup 2})recognized industry leaders in beneficial use during the second annual C{sup 2}P{sup 2} awards ceremony held 23 October 2006 in Atlanta, Georgia. The C{sup 2}P{sup 2} program is led by the EPA with the ACAA, DOE, FHWA, USDA - Agricultural Research Services (ARS), and Utilities Solid Waste Activities Group (USWAG). The award for overall achievement went to Great River Energy of Underwood, ND who partnered with more than 10 public and private organizations to develop an extensive market for fly ash from Coal Creek Station, the world's largest lignite-fired plant. Other awards were given for environmental achievement, innovation, partnership, research and communications and outreach. 9 photos.

Goss, D. [American Coal Ash Association (United States)

2007-07-01

414

Conservation tillage and input use  

Microsoft Academic Search

There continues to be a question as to the overall effectiveness of conservation tillage practices in reducing the impact\\u000a of agricultural production on the environment. While it is generally recognized that water runoff and soil erosion will decline\\u000a further, as tillage and mulch tillage systems are not used more extensively on cropland, what will happen to pesticide and\\u000a fertilizer use

N. D. Uri

1997-01-01

415

[Conservation Units.  

ERIC Educational Resources Information Center

|Instructional units deal with each aspect of conservation: forests, wildlife, r