Identification of distal regulatory regions in the human alpha IIb gene locus necessary for consistent, high-level megakaryocyte expression.

Science.gov (United States)

Thornton, Michael A; Zhang, Chunyan; Kowalska, Maria A; Poncz, Mortimer

2002-11-15

The alphaIIb/beta3-integrin receptor is present at high levels only in megakaryocytes and platelets. Its presence on platelets is critical for hemostasis. The tissue-specific nature of this receptor's expression is secondary to the restricted expression of alphaIIb, and studies of the alphaIIb proximal promoter have served as a model of a megakaryocyte-specific promoter. We have examined the alphaIIb gene locus for distal regulatory elements. Sequence comparison between the human (h) and murine (m) alphaIIb loci revealed high levels of conservation at intergenic regions both 5' and 3' to the alphaIIb gene. Additionally, deoxyribonuclease (DNase) I sensitivity mapping defined tissue-specific hypersensitive (HS) sites that coincide, in part, with these conserved regions. Transgenic mice containing various lengths of the h(alpha)IIb gene locus, which included or excluded the various conserved/HS regions, demonstrated that the proximal promoter was sufficient for tissue specificity, but that a region 2.5 to 7.1 kb upstream of the h(alpha)IIb gene was necessary for consistent expression. Another region 2.2 to 7.4 kb downstream of the gene enhanced expression 1000-fold and led to levels of h(alpha)IIb mRNA that were about 30% of the native m(alpha)IIb mRNA level. These constructs also resulted in detectable h(alpha)IIb/m(beta)3 on the platelet surface. This work not only confirms the importance of the proximal promoter of the alphaIIb gene for tissue specificity, but also characterizes the distal organization of the alphaIIb gene locus and provides an initial localization of 2 important regulatory regions needed for the expression of the alphaIIb gene at high levels during megakaryopoiesis.

Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.

Science.gov (United States)

Wang, Lan; Ren, Shifang; Zhu, Haiyan; Zhang, Dongmei; Hao, Yuqing; Ruan, Yuanyuan; Zhou, Lei; Lee, Chiayu; Qiu, Lin; Yun, Xiaojing; Xie, Jianhui

2012-08-01

CLEC-2 was first identified by sequence similarity to C-type lectin-like molecules with immune functions and has been reported as a receptor for the platelet-aggregating snake venom toxin rhodocytin and the endogenous sialoglycoprotein podoplanin. Recent researches indicate that CLEC-2-deficient mice were lethal at the embryonic stage associated with disorganized and blood-filled lymphatic vessels and severe edema. In view of a necessary role of CLEC-2 in the individual development, it is of interest to investigate its phylogenetic homology and highly conserved functional regions. In this work, we reported that CLEC-2 from different species holds with an extraordinary conservation by sequence alignment and phylogenetic tree analysis. The functional structures including N-linked oligosaccharide sites and ligand-binding domain implement a structural and functional conservation in a variety of species. The glycosylation sites (N120 and N134) are necessary for the surface expression CLEC-2. CLEC-2 from different species possesses the binding activity of mouse podoplanin. Nevertheless, the expression of CLEC-2 is regulated with a species-specific manner. The alternative splicing of pre-mRNA, a regulatory mechanism of gene expression, and the binding sites on promoter for several key transcription factors vary between different species. Therefore, CLEC-2 shares high sequence homology and functional identity. However the transcript expression might be tightly regulated by different mechanisms in evolution.

Telomeric expression sites are highly conserved in Trypanosoma brucei.

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Christiane Hertz-Fowler

Full Text Available Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs. The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology.

Evolutionary conservation and expression of miR-10a-3p in olive flounder and rock bream.

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Jo, Ara; Im, Jennifer; Lee, Hee-Eun; Jang, Dongmin; Nam, Gyu-Hwi; Mishra, Anshuman; Kim, Woo-Jin; Kim, Won; Cha, Hee-Jae; Kim, Heui-Soo

2017-09-10

MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that mainly bind to the seed sequences located within the 3' untranslated region (3' UTR) of target genes. They perform an important biological function as regulators of gene expression. Different genes can be regulated by the same miRNA, whilst different miRNAs can be regulated by the same genes. Here, the evolutionary conservation and expression pattern of miR-10a-3p in olive flounder and rock bream was examined. Binding sites (AAAUUC) to seed region of the 3' UTR of target genes were highly conserved in various species. The expression pattern of miR-10a-3p was ubiquitous in the examined tissues, whilst its expression level was decreased in gill tissues infected by viral hemorrhagic septicemia virus (VHSV) compared to the normal control. In the case of rock bream, the spleen, kidney, and liver tissues showed dominant expression levels of miR-10a-3p. Only the liver tissues in the rock bream samples infected by the iridovirus indicated a dominant miR-10a-3p expression. The gene ontology (GO) analysis of predicted target genes for miR-10a-3p revealed that multiple genes are related to binding activity, catalytic activity, cell components as well as cellular and metabolic process. Overall the results imply that the miR-10a-3p could be used as a biomarker to detect VHSV infection in olive flounder and iridovirus infection in rock bream. In addition, the data provides fundamental information for further study of the complex interaction between miR-10a-3p and gene expression. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

2017-09-01

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

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

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Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they

Importance of uncharged polar residues and proline in the proximal two-thirds (Pro107–Ser128 of the highly conserved region of mouse ileal Na+-dependent bile acid transporter, Slc10a2, in transport activity and cellular expression

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Saeki Tohru

2013-02-01

Full Text Available Abstract Background SLC10A2-mediated reabsorption of bile acids at the distal end of the ileum is the first step in enterohepatic circulation. Because bile acids act not only as detergents but also as signaling molecules in lipid metabolism and energy production, SLC10A2 is important as the key transporter for understanding the in vivo kinetics of bile acids. SLC10A family members and the homologous genes of various species share a highly conserved region corresponding to Gly104–Pro142 of SLC10A2. The functional importance of this region has not been fully elucidated. Results To elucidate the functional importance of this region, we previously performed mutational analysis of the uncharged polar residues and proline in the distal one-third (Thr130–Pro142 of the highly conserved region in mouse Slc10a2. In this study, proline and uncharged polar residues in the remaining two-thirds of this region in mouse Slc10a2 were subjected to mutational analysis, and taurocholic acid uptake and cell surface localization were examined. Cell surface localization of Slc10a2 is necessary for bile acid absorption. Mutants in which Asp or Leu were substituted for Pro107 (P107N or P107L were abundantly expressed, but their cell surface localization was impaired. The S126A mutant was completely impaired in cellular expression. The T110A and S128A mutants exhibited remarkably enhanced membrane expression. The S112A mutant was properly expressed at the cell surface but transport activity was completely lost. Replacement of Tyr117 with various amino acids resulted in reduced transport activity. The degree of reduction roughly depended on the van der Waals volume of the side chains. Conclusions The functional importance of proline and uncharged polar residues in the highly conserved region of mouse Slc10a2 was determined. This information will contribute to the design of bile acid-conjugated prodrugs for efficient drug delivery or SLC10A2 inhibitors for

CORAL: aligning conserved core regions across domain families.

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Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

Conserved structure and expression of hsp70 paralogs in teleost fishes

DEFF Research Database (Denmark)

Metzger, David C.H.; Hansen, Jakob Hemmer; Schulte, Patricia M.

2016-01-01

present in the F. heteroclitus genome. Comparison of expression patterns in F. heteroclitus and Gasterosteus aculeatus demonstrates that hsp70-2 has a higher fold increase than hsp70-1 following heat shock in gill but not in muscle tissue, revealing a conserved difference in expression patterns between...

Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

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Haisheng Nie

Full Text Available BACKGROUND: The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. CONCLUSIONS: The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

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Kohane Isaac

2005-11-01

Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

Developments in conservation tillage in rainfed regions of North China

NARCIS (Netherlands)

Wang, X.B.; Cai, D.X.; Hoogmoed, W.B.; Oenema, O.; Perdok, U.D.

2007-01-01

Dryland regions in northern China account for over 50% of the nation's total area, where farming development is constrained by adverse weather, topography and water resource conditions, low fertility soils, and poor soil management. Conservation tillage research and application in dryland regions of

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

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Nagar, Anurag; Hahsler, Michael

2013-01-01

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

Making the Most of World Natural Heritage—Linking Conservation and Sustainable Regional Development?

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Katharina Conradin

2016-03-01

Full Text Available Today, more than 1000 World Heritage (WH sites are inscribed on UNESCO’s list, 228 of which are natural and mixed heritage sites. Once focused primarily on conservation, World Natural Heritage (WNH sites are increasingly seen as promoters of sustainable regional development. Sustainability-oriented regions, it is assumed, are safeguards for conservation and positively influence local conservation goals. Within UNESCO, discussions regarding the integration of sustainable development in official policies have recently gained momentum. In this article, we investigate the extent to which WNH sites trigger sustainability-oriented approaches in surrounding regions, and how such approaches in turn influence the WNH site and its protection. The results of the study are on the one hand based on a global survey with more than 60% of the WNH sites listed in 2011, and on the other hand on a complementary literature research. Furthermore, we analyze the policy framework necessary to support WNH sites in this endeavor. We conclude that a regional approach to WNH management is necessary to ensure that WNH sites support sustainable regional development effectively, but that the core focus of WNH status must remain environmental conservation.

Flagellar region 3b supports strong expression of integrated DNA and the highest chromosomal integration efficiency of the Escherichia coli flagellar regions.

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Juhas, Mario; Ajioka, James W

2015-07-01

The Gram-negative bacterium Escherichia coli is routinely used as the chassis for a variety of biotechnology and synthetic biology applications. Identification and analysis of reliable chromosomal integration and expression target loci is crucial for E. coli engineering. Chromosomal loci differ significantly in their ability to support integration and expression of the integrated genetic circuits. In this study, we investigate E. coli K12 MG1655 flagellar regions 2 and 3b. Integration of the genetic circuit into seven and nine highly conserved genes of the flagellar regions 2 (motA, motB, flhD, flhE, cheW, cheY and cheZ) and 3b (fliE, F, G, J, K, L, M, P, R), respectively, showed significant variation in their ability to support chromosomal integration and expression of the integrated genetic circuit. While not reducing the growth of the engineered strains, the integrations into all 16 target sites led to the loss of motility. In addition to high expression, the flagellar region 3b supports the highest efficiency of integration of all E. coli K12 MG1655 flagellar regions and is therefore potentially the most suitable for the integration of synthetic genetic circuits. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Turning strategy into action: implementing a conservation action plan in the Cape Floristic Region

CSIR Research Space (South Africa)

Gelderblom, CM

2003-07-01

Full Text Available for conservation. These pressures are predicted to intensify, as the region acts as a magnet for settlement and development. This paper thus describes the development of a conservation action plan for the region, arising from the Cape Action Plan...

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

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Joshi NV

2009-01-01

Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

Regional effects of agricultural conservation practices on nutrient transport in the Upper Mississippi River Basin

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Garcia, Ana Maria.; Alexander, Richard B.; Arnold, Jeffrey G.; Norfleet, Lee; White, Michael J.; Robertson, Dale M.; Schwarz, Gregory E.

2016-01-01

Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to investigate whether spatial differences in conservation intensity were statistically correlated with variations in nutrient loads. In contrast to other forms of water quality data analysis, the application of SPARROW controls for confounding factors such as hydrologic variability, multiple sources and environmental processes. A measure of conservation intensity was derived from the USDA-CEAP regional assessment of the Upper Mississippi River and used as an explanatory variable in a model of the Upper Midwest. The spatial pattern of conservation intensity was negatively correlated (p = 0.003) with the total nitrogen loads in streams in the basin. Total phosphorus loads were weakly negatively correlated with conservation (p = 0.25). Regional nitrogen reductions were estimated to range from 5 to 34% and phosphorus reductions from 1 to 10% in major river basins of the Upper Mississippi region. The statistical associations between conservation and nutrient loads are consistent with hydrological and biogeochemical processes such as denitrification. The results provide empirical evidence at the regional scale that conservation practices have had a larger statistically detectable effect on nitrogen than on phosphorus loadings in streams and rivers of the Upper Mississippi Basin.

Regional Effects of Agricultural Conservation Practices on Nutrient Transport in the Upper Mississippi River Basin.

Science.gov (United States)

García, Ana María; Alexander, Richard B; Arnold, Jeffrey G; Norfleet, Lee; White, Michael J; Robertson, Dale M; Schwarz, Gregory

2016-07-05

Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to investigate whether spatial differences in conservation intensity were statistically correlated with variations in nutrient loads. In contrast to other forms of water quality data analysis, the application of SPARROW controls for confounding factors such as hydrologic variability, multiple sources and environmental processes. A measure of conservation intensity was derived from the USDA-CEAP regional assessment of the Upper Mississippi River and used as an explanatory variable in a model of the Upper Midwest. The spatial pattern of conservation intensity was negatively correlated (p = 0.003) with the total nitrogen loads in streams in the basin. Total phosphorus loads were weakly negatively correlated with conservation (p = 0.25). Regional nitrogen reductions were estimated to range from 5 to 34% and phosphorus reductions from 1 to 10% in major river basins of the Upper Mississippi region. The statistical associations between conservation and nutrient loads are consistent with hydrological and biogeochemical processes such as denitrification. The results provide empirical evidence at the regional scale that conservation practices have had a larger statistically detectable effect on nitrogen than on phosphorus loadings in streams and rivers of the Upper Mississippi Basin.

Fungal conservation: Protected species of fungi in South Serbia region

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Sadiković, D.

2013-12-01

Full Text Available Protection and conservation of fungi has only recently became an issue of concern. Main motives for increased attention are uncontrolled, mass collecting of edible wild mushrooms and environmental pollution which leads to the rapid decline of their natural habitats, some of which are rich with rare and endangered species. By Serbian Nature Conservation Law 2010. there are 38 strictly protected fungal species of which 17 species are recorded in this paper. 11 of those recorded species are on European and/or National Red List of endangered fungal species. All investigated territories were in South Serbia region. This study is a contribution to conservation of protected and threatened fungi and their respective habitats in Serbia.

The relevance of the Mediterranean Region to colonial waterbird conservation

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Erwin, R.M.; Crivelli, Alain J.; Hafner, Heinz; Fasola, Mauro; Erwin, R. Michael; McCrimmon, Donald A.=

1996-01-01

The Mediterranean Sea is the largest partially enclosed sea in the world and provides habitat to more than 100 species of waterbirds from the Palearctic-North African-Middle Eastern regions. Even though the Mediterranean suffers from pollution, has little tidal influence, and is oligotrophic, more than half of the western Palearctic populations of numerous waterfowl species winter in the region. Thirty-three species of colonial waterbirds breed along the 46,000 km Mediterranean coastline with nine species considered threatened or endangered, mostly because of wetland loss and degradation. The long history of human activity and scientific investigations in the region has taught some valuable lessons. In the area of colonial waterbird biology and conservation, we have learned important lessons about the value of long-term monitoring and research on selected populations. From marking studies of Greater Flamingos (Phoenicopterus ruber roseus) and Little Egrets (Egretta garzetta) results have been used to derive useful information about metapopulation dynamics. Involvement of both African and European biologists allowed year-round Studies of these species that yielded valuable spin-offs for training in avian and wetland conservation. We have also learned the value of man-made wetlands as feeding and nesting sites for some colonial waterbirds. Careful evaluations of the habitat quality of different types of wetlands are required, as in contaminant levels such as lead shot and pesticides. Wetland conservationists have also learned from some instructive mistakes. Dam construction and agricultural incentive programs sponsored by the European Community, the World Bank, and others from the past have largely ignored impacts on wetlands and wildlife. In some areas, economic ventures such as aquaculture operations and salt mining have not involved waterbird habitat needs in their planning. Research and conservation needs include: (1) establishing regional monitoring programs and

A trans-national monarch butterfly population model and implications for regional conservation priorities

Science.gov (United States)

Oberhauser, Karen; Wiederholt, Ruscena; Diffendorfer, James E.; Semmens, Darius J.; Ries, Leslie; Thogmartin, Wayne E.; Lopez-Hoffman, Laura; Semmens, Brice

2017-01-01

1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species.2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental-scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippus Linn.) population growth rates.3. We present a spatially explicit demographic model simulating the multi-generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America.4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single-region strategies.5. Synthesis and applications: These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.

The conserved 12-amino acid stretch in the inter-bromodomain region of BET family proteins functions as a nuclear localization signal.

Science.gov (United States)

Fukazawa, Hidesuke; Masumi, Atsuko

2012-01-01

The bromodomain and extraterminal (BET) family is a group of chromatin-binding proteins characterized by two bromodomains, an extraterminal (ET) domain, and several other conserved regions of unknown function. In humans, the BET family consists of four members, BRD2, BRD3, BRD4 and BRDT, that all normally localize to the nucleus. We identified a 12-amino acid stretch in the inter-bromodomain region that is perfectly conserved among the BET family members. We deleted these residues and expressed the mutant proteins in HEK293T cells to investigate the function of this motif. We found that the deletion of this motif alters the localization of BET proteins. Mutated BRD3 and BRD4 were excluded from the nucleus, and BRDT was found to be diffused throughout the nucleus and cytoplasm. Although the mutant BRD2 remained predominantly in the nucleus, a punctate distribution was also observed in the cytosol. It has been reported that a conserved motif between the second bromodomain and the ET domain serves as a nuclear localization signal for BRD2. Nevertheless, BET mutants lacking the reported nuclear localization signal motif but retaining the 12-amino acid stretch resided in the nucleus. Furthermore, these mutants were diffused throughout the cytoplasm when the 12 residues were removed. These results indicate that the conserved amino acid stretch in the inter-bromodomain region of the BET family functions as a nuclear localization signal.

A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions.

Science.gov (United States)

Pavlacky, David C; Lukacs, Paul M; Blakesley, Jennifer A; Skorkowsky, Robert C; Klute, David S; Hahn, Beth A; Dreitz, Victoria J; George, T Luke; Hanni, David J

2017-01-01

Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1) coordination across organizations and regions, 2) meaningful management and conservation objectives, and 3) rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR) program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17). We provide two examples for the Brewer's sparrow (Spizella breweri) in BCR 17 demonstrating the ability of the design to 1) determine hierarchical population responses to landscape change and 2) estimate hierarchical habitat relationships to predict the response of the Brewer's sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous statistical

A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions.

Directory of Open Access Journals (Sweden)

David C Pavlacky

Full Text Available Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1 coordination across organizations and regions, 2 meaningful management and conservation objectives, and 3 rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17. We provide two examples for the Brewer's sparrow (Spizella breweri in BCR 17 demonstrating the ability of the design to 1 determine hierarchical population responses to landscape change and 2 estimate hierarchical habitat relationships to predict the response of the Brewer's sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous

Conservation status of the American horseshoe crab, (Limulus polyphemus): A regional assessment

Science.gov (United States)

Smith, David R.; Brockmann, H. Jane; Beekey, Mark A.; King, Timothy L.; Millard, Michael J.; Zaldívar-Rae, Jaime

2017-01-01

Horseshoe crabs have persisted for more than 200 million years, and fossil forms date to 450 million years ago. The American horseshoe crab (Limulus polyphemus), one of four extant horseshoe crab species, is found along the Atlantic coastline of North America ranging from Alabama to Maine, USA with another distinct population on the coasts of Campeche, Yucatán and Quintana Roo in the Yucatán Peninsula, México. Although the American horseshoe crab tolerates broad environmental conditions, exploitation and habitat loss threaten the species. We assessed the conservation status of the American horseshoe crab by comprehensively reviewing available scientific information on its range, life history, genetic structure, population trends and analyses, major threats, and conservation. We structured the status assessment by six genetically-informed regions and accounted for sub-regional differences in environmental conditions, threats, and management. The transnational regions are Gulf of Maine (USA), Mid-Atlantic (USA), Southeast (USA), Florida Atlantic (USA), Northeast Gulf of México (USA), and Yucatán Peninsula (México). Our conclusion is that the American horseshoe crab species is vulnerable to local extirpation and that the degree and extent of risk vary among and within the regions. The risk is elevated in the Gulf of Maine region due to limited and fragmented habitat. The populations of horseshoe crabs in the Mid-Atlantic region are stable in the Delaware Bay area, and regulatory controls are in place, but the risk is elevated in the New England area as evidenced by continuing declines understood to be caused by over-harvest. The populations of horseshoe crabs in the Southeast region are stable or increasing. The populations of horseshoe crabs in the Florida Atlantic region show mixed trends among areas, and continuing population reductions at the embayment level have poorly understood causes. Within the Northeast Gulf of Mexico, causes of population trends are

High-resolution temporal and regional mapping of MAPT expression and splicing in human brain development.

Science.gov (United States)

Hefti, Marco M; Farrell, Kurt; Kim, SoongHo; Bowles, Kathryn R; Fowkes, Mary E; Raj, Towfique; Crary, John F

2018-01-01

The microtubule associated protein tau plays a critical role in the pathogenesis of neurodegenerative disease. Recent studies suggest that tau also plays a role in disorders of neuronal connectivity, including epilepsy and post-traumatic stress disorder. Animal studies have shown that the MAPT gene, which codes for the tau protein, undergoes complex pre-mRNA alternative splicing to produce multiple isoforms during brain development. Human data, particularly on temporal and regional variation in tau splicing during development are however lacking. In this study, we present the first detailed examination of the temporal and regional sequence of MAPT alternative splicing in the developing human brain. We used a novel computational analysis of large transcriptomic datasets (total n = 502 patients), quantitative polymerase chain reaction (qPCR) and western blotting to examine tau expression and splicing in post-mortem human fetal, pediatric and adult brains. We found that MAPT exons 2 and 10 undergo abrupt shifts in expression during the perinatal period that are unique in the canonical human microtubule-associated protein family, while exon 3 showed small but significant temporal variation. Tau isoform expression may be a marker of neuronal maturation, temporally correlated with the onset of axonal growth. Immature brain regions such as the ganglionic eminence and rhombic lip had very low tau expression, but within more mature regions, there was little variation in tau expression or splicing. We thus demonstrate an abrupt, evolutionarily conserved shift in tau isoform expression during the human perinatal period that may be due to tau expression in maturing neurons. Alternative splicing of the MAPT pre-mRNA may play a vital role in normal brain development across multiple species and provides a basis for future investigations into the developmental and pathological functions of the tau protein.

Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

Science.gov (United States)

Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

2009-01-01

Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

CO2 emissions reduction using energy conservation measures: EPA Region IV's experience

International Nuclear Information System (INIS)

Berish, C.; Day, R.; Sibold, K.; Tiller, J.

1994-01-01

EPA Region 4 concluded in a recent comparative environmental risk evaluation that global climate change could substantially impact the Southeast. To address this risk, Region 4 developed an action plan to promote cost-effective pollution prevention and reduce greenhouse gas emissions, The regional plan contains programs that aye specific to Region 4 as well as geographic components of the national Climate Change Action Plan. Sources of carbon dioxide emissions were targeted for pollution prevention based on an energy model that allows the user to create energy efficiency scenarios in four sectors: residential, commercial, industrial, and transportation. Activities were selected using the modeled information on sector reduction potentials and resource and cost-effectiveness criteria. Given the high level of uncertainty associated with climate change projections, the programs developed are all cost effective, prevent pollution and/or result in sound adaptation policies. Currently, policy makers at national, regional, and local levels are deciding on what types of energy efficiency programs to implement. The region's action plan is composed of several programs and approaches. The authors have developed implemented, and/or participated in the following: energy scenario model. EARTHWALK (residential energy conservation); energy conservation in affordable homes (new residences); Cool Communities Program (strategic tree planting and light colored surfaces); EPA's Green Lights Program; WAVE (water conservation), the Plant Protection Center; QUEST TO SAVE THE EARTH (outreach tools); energy and water use planning for the 1996 Olympic Games, and planning for sea-level rise. Reviewing the practices of the above programs will be the focus of this paper

Brain region-dependent differential expression of alpha-synuclein.

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Taguchi, Katsutoshi; Watanabe, Yoshihisa; Tsujimura, Atsushi; Tanaka, Masaki

2016-04-15

α-Synuclein, the major constituent of Lewy bodies (LBs), is normally expressed in presynapses and is involved in synaptic function. Abnormal intracellular aggregation of α-synuclein is observed as LBs and Lewy neurites in neurodegenerative disorders, such as Parkinson's disease (PD) or dementia with Lewy bodies. Accumulated evidence suggests that abundant intracellular expression of α-synuclein is one of the risk factors for pathological aggregation. Recently, we reported differential expression patterns of α-synuclein between excitatory and inhibitory hippocampal neurons. Here we further investigated the precise expression profile in the adult mouse brain with special reference to vulnerable regions along the progression of idiopathic PD. The results show that α-synuclein was highly expressed in the neuronal cell bodies of some early PD-affected brain regions, such as the olfactory bulb, dorsal motor nucleus of the vagus, and substantia nigra pars compacta. Synaptic expression of α-synuclein was mostly accompanied by expression of vesicular glutamate transporter-1, an excitatory presynaptic marker. In contrast, expression of α-synuclein in the GABAergic inhibitory synapses was different among brain regions. α-Synuclein was clearly expressed in inhibitory synapses in the external plexiform layer of the olfactory bulb, globus pallidus, and substantia nigra pars reticulata, but not in the cerebral cortex, subthalamic nucleus, or thalamus. These results suggest that some neurons in early PD-affected human brain regions express high levels of perikaryal α-synuclein, as happens in the mouse brain. Additionally, synaptic profiles expressing α-synuclein are different in various brain regions. © 2015 Wiley Periodicals, Inc.

Homologous high-throughput expression and purification of highly conserved E coli proteins

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Duchmann Rainer

2007-06-01

Full Text Available Abstract Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD. Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP, N-utilizing substance A (NusA, or glutathione S-transferase (GST to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS. Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500

Redeployment of germ layers related TFs shows regionalized expression during two non-embryonic developments.

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Ricci, Lorenzo; Cabrera, Fabien; Lotito, Sonia; Tiozzo, Stefano

2016-08-01

In all non-vertebrate metazoan phyla, species that evolved non-embryonic developmental pathways as means of propagation or regeneration can be found. In this context, new bodies arise through asexual reproduction processes (such as budding) or whole body regeneration, that lack the familiar temporal and spatial cues classically associated with embryogenesis, like maternal determinants, or gastrulation. The molecular mechanisms underlying those non-embryonic developments (i.e., regeneration and asexual reproduction), and their relationship to those deployed during embryogenesis are poorly understood. We have addressed this question in the colonial ascidian Botryllus schlosseri, which undergoes an asexual reproductive process via palleal budding (PB), as well as a whole body regeneration by vascular budding (VB). We identified early regenerative structures during VB and then followed the fate of differentiating tissues during both non-embryonic developments (PB and VB) by monitoring the expression of genes known to play key functions in germ layer specification with well conserved expression patterns in solitary ascidian embryogenesis. The expression patterns of FoxA1, GATAa, GATAb, Otx, Bra, Gsc and Tbx2/3 were analysed during both PB and VB. We found that the majority of these transcription factors were expressed during both non-embryonic developmental processes, revealing a regionalization of the palleal and vascular buds. Knockdown of GATAa by siRNA in palleal buds confirmed that preventing the correct development of one of these regions blocks further tissue specification. Our results indicate that during both normal and injury-induced budding, a similar alternative developmental program operates via early commitment of epithelial regions. Copyright © 2016. Published by Elsevier Inc.

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

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Pesole Graziano

2007-02-01

Full Text Available Abstract Background This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. Results We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers. Conclusion Results of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the genes.

Lessons from Transportation Agency Participation In Regional Conservation Initiatives

OpenAIRE

Lederman, Jaimee

2017-01-01

Transportation agencies struggle to maximize the benefits of transportation infrastructure while minimizing environmental harm. This dissertation examines institutional collaborations that integrate capital investments (e.g. highway and rail projects) with regional Habitat Conservation Plans (RHCPs) under the Endangered Species Act (ESA). It addresses ways of maintaining these collaborations over time. The ESA requires that public and private project developers mitigate any harm to endangered...

Global conservation model for a mushy region over a moving substrate

Czech Academy of Sciences Publication Activity Database

Kyselica, Juraj; Šimkanin, Ján

2018-01-01

Roč. 276, March (2018), s. 60-67 ISSN 0031-9201 Institutional support: RVO:67985530 Keywords : solidification * binary alloy * mushy region * global conservation * boundary-layer flow Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 2.075, year: 2016

The identification and functional annotation of RNA structures conserved in vertebrates

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

2017-01-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure...... (RBPs) or (ii) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared...... expression and shared structure despite low abundance and low sequence identity. About 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured...

Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting

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Marcos De Donato

2017-06-01

Full Text Available KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS, but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements, compared with their whole chromosomes (detected by RepeatMasker. The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista, such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70% between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor–binding sites. We detected several transcription factors (using JASPAR suite from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be

Conservation in metropolitan regions: assessing trends and threats of urban development and climate change

Science.gov (United States)

Thorne, J. H.; Santos, M. J.; Bjorkman, J.

2011-12-01

Two global challenges to successful conservation are urban expansion and climate change. Rapid urban growth threatens biodiversity and associated ecosystem services, while climate change may make currently protected areas unsuitable for species that exist within them. We examined three measures of landscape change for 8800 km2 of the San Francisco Bay metropolitan region over 80 years past and future: urban growth, protected area establishment, and natural vegetation type extents. The Bay Area is a good test bed for conservation assessment of the impacts of temporal and spatial of urban growth and land cover change. The region is geographically rather small, with over 40% of its lands already dedicated to protected park and open space lands, they are well-documented, and, the area has had extensive population growth in the past and is projected to continue to grow. The ten-county region within which our study area is a subset has grown from 1.78 million people in 1930, to 6.97 million in 2000 and is estimated to grow to 10.94 million by 2050. With such an influx of people into a small geographic area, it is imperative to both examine the past urban expansion and estimate how the future population will be accommodated into the landscape. We quantify these trends to assess conservation 'success' through time. We used historical and current landcover maps to assess trend, and a GIS-based urban modeling (UPlan) to assess future urban growth impacts in the region, under three policy scenarios- business as usual, smart growth, and urban redevelopment. Impacts are measured by the amount of open space targeted by conservation planners in the region that will be urbanized under each urban growth policy. Impacts are also measured by estimates of the energy consumption projected for each of the scenarios on household and business unit level. The 'business as usual' and 'smart growth' scenarios differed little in their impacts to targeted conservation lands, because so little

Federal Conservation Units in Brazil: The Situation of Biomes and Regions

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Eduardo Pacca Luna Mattar

2018-03-01

Full Text Available ABSTRACT Federal conservation units (FCU are areas legally established by the government, in order to meet the needs of protection and sustainable exploitation of biodiversity. A way to ensure the efficiency of public management is to systematize data. Therefore, the present study grouped and analyzed public data about FCU. Brazil has 309 federal conservation units, which represent 9.06% of the national territory and 45305 residents households. The Northern Region covers 84.80% of these families and 79.20% of its area belongs to FCU. The Amazônia biome has 14.57% of its territory occupied by FCU; on the other hand, Pantanal has only 0.98% of its area protected. There is a higher concentration of public agents in the FCU of the Southeastern region and in the Mata Atlântica biome. The analysis of this information reveals significant differences between the biomes and the federation units, a fact that reflects the importance of the organization of public data.

Motor fuel taxation, energy conservation, and economic development: A regional approach

International Nuclear Information System (INIS)

England, Richard W.

2007-01-01

Combustion of motor fuels has a variety of environmental impacts on local, regional and global scales. Taxing motor fuels more heavily would mitigate those environmental impacts. However, many governments are reluctant to increase motor fuel taxes because they fear that the tax incidence will be regressive and that economic development will be impeded. Using data for the New England region of the United States, this paper argues that an oil-importing region can conserve energy, avoid regressive impacts and encourage economic development by taxing motor fuels more heavily and rebating the incremental revenues to owners of motor vehicles. (author)

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.

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Colin R Lickwar

2017-08-01

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

Identification of an evolutionarily conserved extracellular threonine residue critical for surface expression and its potential coupling of adjacent voltage-sensing and gating domains in voltage-gated potassium channels.

Science.gov (United States)

Mckeown, Lynn; Burnham, Matthew P; Hodson, Charlotte; Jones, Owen T

2008-10-31

The dynamic expression of voltage-gated potassium channels (Kvs) at the cell surface is a fundamental factor controlling membrane excitability. In exploring possible mechanisms controlling Kv surface expression, we identified a region in the extracellular linker between the first and second of the six (S1-S6) transmembrane-spanning domains of the Kv1.4 channel, which we hypothesized to be critical for its biogenesis. Using immunofluorescence microscopy, flow cytometry, patch clamp electrophysiology, and mutagenesis, we identified a single threonine residue at position 330 within the Kv1.4 S1-S2 linker that is absolutely required for cell surface expression. Mutation of Thr-330 to an alanine, aspartate, or lysine prevented surface expression. However, surface expression occurred upon co-expression of mutant and wild type Kv1.4 subunits or mutation of Thr-330 to a serine. Mutation of the corresponding residue (Thr-211) in Kv3.1 to alanine also caused intracellular retention, suggesting that the conserved threonine plays a generalized role in surface expression. In support of this idea, sequence comparisons showed conservation of the critical threonine in all Kv families and in organisms across the evolutionary spectrum. Based upon the Kv1.2 crystal structure, further mutagenesis, and the partial restoration of surface expression in an electrostatic T330K bridging mutant, we suggest that Thr-330 hydrogen bonds to equally conserved outer pore residues, which may include a glutamate at position 502 that is also critical for surface expression. We propose that Thr-330 serves to interlock the voltage-sensing and gating domains of adjacent monomers, thereby yielding a structure competent for the surface expression of functional tetramers.

An evolutionarily conserved sexual signature in the primate brain.

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Björn Reinius

2008-06-01

Full Text Available The question of a potential biological sexual signature in the human brain is a heavily disputed subject. In order to provide further insight into this issue, we used an evolutionary approach to identify genes with sex differences in brain expression level among primates. We reasoned that expression patterns important to uphold key male and female characteristics may be conserved during evolution. We selected cortex for our studies because this specific brain region is responsible for many higher behavioral functions. We compared gene expression profiles in the occipital cortex of male and female humans (Homo sapiens, a great ape and cynomolgus macaques (Macaca fascicularis, an old world monkey, two catarrhine species that show abundant morphological sexual dimorphism, as well as in common marmosets (Callithrix Jacchus, a new world monkey which are relatively sexually monomorphic. We identified hundreds of genes with sex-biased expression patterns in humans and macaques, while fewer than ten were differentially expressed between the sexes in marmosets. In primates, a general rule is that many of the morphological and behavioral sexual dimorphisms seen in polygamous species, such as macaques, are typically less pronounced in monogamous species such as the marmosets. Our observations suggest that this correlation may also be reflected in the extent of sex-biased gene expression in the brain. We identified 85 genes with common sex-biased expression, in both human and macaque and 2 genes, X inactivation-specific transcript (XIST and Heat shock factor binding protein 1 (HSBP1, that were consistently sex-biased in the female direction in human, macaque, and marmoset. These observations imply a conserved signature of sexual gene expression dimorphism in cortex of primates. Further, we found that the coding region of female-biased genes is more evolutionarily constrained compared to the coding region of both male-biased and non sex-biased brain

Building on IUCN regional red lists to produce lists of species of conservation priority: a model with Irish bees.

Science.gov (United States)

Fitzpatrick, Una; Murray, Tomás E; Paxton, Robert J; Brown, Mark J F

2007-10-01

A World Conservation Union (IUCN) regional red list is an objective assessment of regional extinction risk and is not the same as a list of conservation priority species. Recent research reveals the widespread, but incorrect, assumption that IUCN Red List categories represent a hierarchical list of priorities for conservation action. We developed a simple eight-step priority-setting process and applied it to the conservation of bees in Ireland. Our model is based on the national red list but also considers the global significance of the national population; the conservation status at global, continental, and regional levels; key biological, economic, and societal factors; and is compatible with existing conservation agreements and legislation. Throughout Ireland, almost one-third of the bee fauna is threatened (30 of 100 species), but our methodology resulted in a reduced list of only 17 priority species. We did not use the priority species list to broadly categorize species to the conservation action required; instead, we indicated the individual action required for all threatened, near-threatened, and data-deficient species on the national red list based on the IUCN's conservation-actions template file. Priority species lists will strongly influence prioritization of conservation actions at national levels, but action should not be exclusive to listed species. In addition, all species on this list will not necessarily require immediate action. Our method is transparent, reproducible, and readily applicable to other taxa and regions.

Exploring spatial patterns of vulnerability for diverse biodiversity descriptors in regional conservation planning.

Science.gov (United States)

Vimal, Ruppert; Pluvinet, Pascal; Sacca, Céline; Mazagol, Pierre-Olivier; Etlicher, Bernard; Thompson, John D

2012-03-01

In this study, we developed a multi-criteria assessment of spatial variability of the vulnerability of three different biodiversity descriptors: sites of high conservation interest by virtue of the presence of rare or remarkable species, extensive areas of high ecological integrity, and landscape diversity in grid cells across an entire region. We assessed vulnerability in relation to (a) direct threats in and around sites to a distance of 2 km associated with intensive agriculture, building and road infrastructure and (b) indirect effects of human population density on a wider scale (50 km). The different combinations of biodiversity and threat indicators allowed us to set differential priorities for biodiversity conservation and assess their spatial variation. For example, with this method we identified sites and grid cells which combined high biodiversity with either high threat values or low threat values for the three different biodiversity indicators. In these two classes the priorities for conservation planning will be different, reduce threat values in the former and restrain any increase in the latter. We also identified low priority sites (low biodiversity with either high or low threats). This procedure thus allows for the integration of a spatial ranking of vulnerability into priority setting for regional conservation planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

Energy Conservation and Development Plan. Southern Tier Central Region, New York

Energy Technology Data Exchange (ETDEWEB)

1979-07-01

A summary is presented of the work of 40 volunteers working with regional planners to imagine, assess, and prescribe for the development of local energy resources (wind, solar, biomass, and water) and for conservation of all forms of energy. The plan contains a brief summary of the process the citizens followed in formulating the plan, the plans themselves, and appendices which contain more detailed comments by citizens on the possible consequences of the development of each resource. The areas (Chemung, Steuben, and Schuyler counties) experienced severe natural gas curtailments during the winter of 1976-1977. The formulation of an emergency energy conservation plan is also presented.

Vascular Gene Expression: A Hypothesis

Directory of Open Access Journals (Sweden)

Angélica Concepción eMartínez-Navarro

2013-07-01

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

Identifying Regulatory Patterns at the 3'end Regions of Over-expressed and Under-expressed Genes

KAUST Repository

Othoum, Ghofran K

2013-05-01

Promoters, neighboring regulatory regions and those extending further upstream of the 5’end of genes, are considered one of the main components affecting the expression status of genes in a specific phenotype. More recently research by Chen et al. (2006, 2012) and Mapendano et al. (2010) demonstrated that the 3’end regulatory regions of genes also influence gene expression. However, the association between the regulatory regions surrounding 3’end of genes and their over- or under-expression status in a particular phenotype has not been systematically studied. The aim of this study is to ascertain if regulatory regions surrounding the 3’end of genes contain sufficient regulatory information to correlate genes with their expression status in a particular phenotype. Over- and under-expressed ovarian cancer (OC) genes were used as a model. Exploratory analysis of the 3’end regions were performed by transforming the annotated regions using principal component analysis (PCA), followed by clustering the transformed data thereby achieving a clear separation of genes with different expression status. Additionally, several classification algorithms such as Naïve Bayes, Random Forest and Support Vector Machine (SVM) were tested with different parameter settings to analyze the discriminatory capacity of the 3’end regions of genes related to their gene expression status. The best performance was achieved using the SVM classification model with 10-fold cross-validation that yielded an accuracy of 98.4%, sensitivity of 99.5% and specificity of 92.5%. For gene expression status for newly available instances, based on information derived from the 3’end regions, an SVM predictive model was developed with 10-fold cross-validation that yielded an accuracy of 67.0%, sensitivity of 73.2% and specificity of 61.0%. Moreover, building an SVM with polynomial kernel model to PCA transformed data yielded an accuracy of 83.1%, sensitivity of 92.5% and specificity of 74.8% using

Identifying Regulatory Patterns at the 3'end Regions of Over-expressed and Under-expressed Genes

KAUST Repository

Othoum, Ghofran K

2013-01-01

Promoters, neighboring regulatory regions and those extending further upstream of the 5’end of genes, are considered one of the main components affecting the expression status of genes in a specific phenotype. More recently research by Chen et al. (2006, 2012) and Mapendano et al. (2010) demonstrated that the 3’end regulatory regions of genes also influence gene expression. However, the association between the regulatory regions surrounding 3’end of genes and their over- or under-expression status in a particular phenotype has not been systematically studied. The aim of this study is to ascertain if regulatory regions surrounding the 3’end of genes contain sufficient regulatory information to correlate genes with their expression status in a particular phenotype. Over- and under-expressed ovarian cancer (OC) genes were used as a model. Exploratory analysis of the 3’end regions were performed by transforming the annotated regions using principal component analysis (PCA), followed by clustering the transformed data thereby achieving a clear separation of genes with different expression status. Additionally, several classification algorithms such as Naïve Bayes, Random Forest and Support Vector Machine (SVM) were tested with different parameter settings to analyze the discriminatory capacity of the 3’end regions of genes related to their gene expression status. The best performance was achieved using the SVM classification model with 10-fold cross-validation that yielded an accuracy of 98.4%, sensitivity of 99.5% and specificity of 92.5%. For gene expression status for newly available instances, based on information derived from the 3’end regions, an SVM predictive model was developed with 10-fold cross-validation that yielded an accuracy of 67.0%, sensitivity of 73.2% and specificity of 61.0%. Moreover, building an SVM with polynomial kernel model to PCA transformed data yielded an accuracy of 83.1%, sensitivity of 92.5% and specificity of 74.8% using

The research on regional conservation planning of urban historical and cultural areas based on GIS

Science.gov (United States)

Li, Shangli; Xu, Jian; Li, Qian

2017-06-01

With the rapid economic development and the growth of population happening in the urban historical and cultural areas, heritage and historical buildings along with their natural and artificial surrounding environments are suffering constructive destruction. Due to the lack of precise partition of protection region and construction control region in the local cultural relics protection law, traditional regional conservation planning cannot engaged with the urban controllability detailed planning very well. According to the several protection regulations about heritage and historical buildings from latest laws, we choose Baxian Temple area to study on the improvments of traditional regional conservation planning. The technical methods of this study mainly rely on GIS, which can complete the fundamental work of each stage. With the analytic hierarchy process(AHP), the comprehensive architectural value assessments can be calculated according to the investigation results. Based on the calculation results and visual corridor analysis, the precise range of protection region and construction control region can be decided and the specific protection measures can be formulated.

Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs

DEFF Research Database (Denmark)

Olsen, Addie Nina; Mundy, John; Skriver, Karen

2002-01-01

Arabidopsis family of 34 genes. The predicted peptides are characterized by a conserved C-terminal sequence motif and additional primary structure conservation in a core region. The majority of these genes had not previously been annotated. A subset of the predicted peptides show high overall sequence...... similarity to Rapid Alkalinization Factor (RALF), a peptide isolated from tobacco. We therefore refer to this peptide family as RALFL for RALF-Like. RT-PCR analysis confirmed that several of the Arabidopsis genes are expressed and that their expression patterns vary. The identification of a large gene family...

Usherin expression is highly conserved in mouse and human tissues.

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Pearsall, Nicole; Bhattacharya, Gautam; Wisecarver, Jim; Adams, Joe; Cosgrove, Dominic; Kimberling, William

2002-12-01

Usher syndrome is an autosomal recessive disease that results in varying degrees of hearing loss and retinitis pigmentosa. Three types of Usher syndrome (I, II, and III) have been identified clinically with Usher type II being the most common of the three types. Usher type II has been localized to three different chromosomes 1q41, 3p, and 5q, corresponding to Usher type 2A, 2B, and 2C respectively. Usherin is a basement membrane protein encoded by the USH2A gene. Expression of usherin has been localized in the basement membrane of several tissues, however it is not ubiquitous. Immunohistochemistry detected usherin in the following human tissues: retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus, and testis. Usherin was absent in many other tissues such as heart, lung, liver, kidney, and brain. This distribution is consistent with the usherin distribution seen in the mouse. Conservation of usherin is also seen at the nucleotide and amino acid level when comparing the mouse and human gene sequences. Evolutionary conservation of usherin expression at the molecular level and in tissues unaffected by Usher 2a supports the important structural and functional role this protein plays in the human. In addition, we believe that these results could lead to a diagnostic procedure for the detection of Usher syndrome and those who carry an USH2A mutation.

Development of a landscape integrity model framework to support regional conservation planning.

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Walston, Leroy J; Hartmann, Heidi M

2018-01-01

Land managers increasingly rely upon landscape assessments to understand the status of natural resources and identify conservation priorities. Many of these landscape planning efforts rely on geospatial models that characterize the ecological integrity of the landscape. These general models utilize measures of habitat disturbance and human activity to map indices of ecological integrity. We built upon these modeling frameworks by developing a Landscape Integrity Index (LII) model using geospatial datasets of the human footprint, as well as incorporation of other indicators of ecological integrity such as biodiversity and vegetation departure. Our LII model serves as a general indicator of ecological integrity in a regional context of human activity, biodiversity, and change in habitat composition. We also discuss the application of the LII framework in two related coarse-filter landscape conservation approaches to expand the size and connectedness of protected areas as regional mitigation for anticipated land-use changes.

The identification and functional annotation of RNA structures conserved in vertebrates.

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Seemann, Stefan E; Mirza, Aashiq H; Hansen, Claus; Bang-Berthelsen, Claus H; Garde, Christian; Christensen-Dalsgaard, Mikkel; Torarinsson, Elfar; Yao, Zizhen; Workman, Christopher T; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L; Gorodkin, Jan

2017-08-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality. © 2017 Seemann et al.; Published by Cold Spring Harbor Laboratory Press.

Regional Conservation Status of Scleractinian Coral Biodiversity in the Republic of the Marshall Islands

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Zoe Richards

2013-07-01

Full Text Available Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss, but they must be undertaken with precise information at an appropriate spatial scale to provide accurate classifications. Here we explore the regional conservation status of scleractinian corals on isolated Pacific Ocean atolls in the Republic of the Marshall Islands. We compile an integrated regional species list based upon new and historical records, and compare how well the regional threat classifications reflect species level priorities at a global scale. A similar proportion of the 240 species of hard coral recorded in the current survey are classified as Vulnerable at the regional scale as the global scale using the International Union for the Conservation of Nature (IUCN Red List criteria (23% and 20% respectively, however there are distinct differences in the composition of species. When local abundance data is taken into account, a far greater proportion of the regional diversity (up to 80% may face an elevated risk of local extinction. These results suggest coral communities on isolated Pacific coral reefs, which are often predicted to be at low risk, are still vulnerable due to the small and fragmented nature of their populations. This reinforces that to adequately protect biodiversity, ongoing threatened species monitoring and the documentation of species-level changes in abundance and distribution is imperative.

DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.

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Zhiheng Wang

Full Text Available The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database.The DisoMCS is available at http://cal.tongji.edu.cn/disorder/.

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

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

2011-04-26

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

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

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Ying Chen

2011-04-01

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

Cellular and tissue expression of DAPIT, a phylogenetically conserved peptide

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H. Kontro

2012-05-01

Full Text Available DAPIT (Diabetes Associated Protein in Insulin-sensitive Tissues is a small, phylogenetically conserved, 58 amino acid peptide that was previously shown to be down-regulated at mRNA level in insulin-sensitive tissues of type 1 diabetes rats. In this study we characterize a custom made antibody against DAPIT and confirm the mitochondrial presence of DAPIT on cellular level. We also show that DAPIT is localized in lysosomes of HUVEC and HEK 293T cells. In addition, we describe the histological expression of DAPIT in several tissues of rat and man and show that it is highly expressed especially in cells with high aerobic metabolism and epithelial cells related to active transport of nutrients and ions. We propose that DAPIT, in addition to indicated subunit of mitochondrial F-ATPase, is also a subunit of lysosomal V-ATPase suggesting that it is a common component in different proton pumps.

Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis.

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Pouillot, Flavie; Fayolle, Corinne; Carniel, Elisabeth

2008-10-01

The transformation of the enteropathogenic bacterium Yersinia pseudotuberculosis into the plague bacillus, Yersinia pestis, has been accompanied by extensive genetic loss. This study focused on chromosomal regions conserved in Y. pseudotuberculosis and lost during its transformation into Y. pestis. An extensive PCR screening of 78 strains of the two species identified five regions (R1 to R5) and four open reading frames (ORFs; orf1 to orf4) that were conserved in Y. pseudotuberculosis and absent from Y. pestis. Their conservation in Y. pseudotuberculosis suggests a positive selective pressure and a role during the life cycle of this species. Attempts to delete two ORFs (orf3 and orf4) from the chromosome of strain IP32953 were unsuccessful, indicating that they are essential for its viability. The seven remaining loci were individually deleted from the IP32953 chromosome, and the ability of each mutant to grow in vitro and to kill mice upon intragastric infection was evaluated. Four loci (orf1, R2, R4, and R5) were not required for optimal growth or virulence of Y. pseudotuberculosis. In contrast, orf2, encoding a putative pseudouridylate synthase involved in RNA stability, was necessary for the optimal growth of IP32953 at 37 degrees C in a chemically defined medium (M63S). Deletion of R1, a region predicted to encode the methionine salvage pathway, altered the mutant pathogenicity, suggesting that the availability of free methionine is severely restricted in vivo. R3, a region composed mostly of genes of unknown functions, was necessary for both optimal growth of Y. pseudotuberculosis at 37 degrees C in M63S and for virulence. Therefore, despite their loss in Y. pestis, five of the nine Y. pseudotuberculosis-specific chromosomal loci studied play a role in the survival, growth, or virulence of this species.

A distal region of the human TGM1 promoter is required for expression in transgenic mice and cultured keratinocytes

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Lu Ying

2004-04-01

transcriptional activity. Conclusions A distal region of the TGM1 gene promoter, containing AP1 and Sp1 binding sites, is evolutionarily conserved and responsible for high level expression in transgenic mice and in transfected keratinocyte cultures.

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

Science.gov (United States)

Ando, Amy W; Mallory, Mindy L

2012-04-24

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.

Evidence for in vitro and in vivo expression of the conserved VAR3 (type 3) plasmodium falciparum erythrocyte membrane protein 1

DEFF Research Database (Denmark)

Wang, Christian W; Lavstsen, Thomas; Bengtsson, Dominique C

2012-01-01

ABSTRACT: BACKGROUND: Members of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion antigen family are major contributors to the pathogenesis of P. falciparum malaria infections. The PfEMP1-encoding var genes are among the most diverse sequences in nature, but three genes......, var1, var2csa and var3 are found conserved in most parasite genomes. The most severe forms of malaria disease are caused by parasites expressing a subset of antigenically conserved PfEMP1 variants. Thus the ubiquitous and conserved VAR3 PfEMP1 is of particular interest to the research field. Evidence...... of VAR3 expression on the infected erythrocyte surface has never been presented, and var3 genes have been proposed to be transcribed and expressed differently from the rest of the var gene family members. METHODS: In this study, parasites expressing VAR3 PfEMP1 were generated using anti-VAR3 antibodies...

Effects of flux conservation on the field configuration in Scyllac

International Nuclear Information System (INIS)

Van der Laan, P.C.T.

1977-04-01

Flux conservation in Scyllac-type experiments shows up in two ways. First of all the poloidal flux between the outside edge of the plasma and the inside of the coil is conserved. This requires a net longitudinal current in the plasma, to cancel the poloidal flux caused by the helical stellarator fields. An expression for this net current is derived, and effects that could occur in sector experiments are discussed. The flux conservation inside the conducting plasma leads to a conservation of the local rotational transform. Since the pinch itself is surrounded by a well-conducting low-density plasma, the rotational transform is conserved in a wide region. Depending on the time history of the applied fields, volume currents are induced in this region, as is shown for two examples. Although an additional capacitor bank can be used to cancel the net current, a cancellation of all the volume currents is extremely difficult. The resulting equilibrium configurations differ considerably from the Scyllac equilibria without volume currents, which are used in stability calculations

An evolutionary model for protein-coding regions with conserved RNA structure

DEFF Research Database (Denmark)

Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

2004-01-01

in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume...... components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

Local knowledge of the flora of a region: implications in biodiversity conservation

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Maria da Conceição Pereira

2016-11-01

Full Text Available The flora of a region is important in aesthetic, environmental and economic terms. Academic degree holders are fundamental for the sustainable development of a geographically isolated region such as the Azores, the University of Azores (UAc contributing to that goal. We assessed the perception of the UAc students about the origin and the importance of the Azorean flora for conservation, culture and economy, by applying a questionnaire to 309 students in different scientific areas, addressing origin, symbolic importance, economic importance, and environmental functions. Students showed some knowledge about the concepts of endemic, native, introduced and invasive species, but often failed to connect those to specific plant taxa. Most species cited as symbolic were animals, and the plants mentioned were mainly exotic/invasive. Respondents had a sense of the most important crops and forest species, and attributed several functions related to biodiversity and environmental conservation to the flora. Despite the many actions already implemented, more initiatives are required to increase the connection between Azoreans and Azorean flora.

TOPAZ1, a novel germ cell-specific expressed gene conserved during evolution across vertebrates.

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Adrienne Baillet

Full Text Available BACKGROUND: We had previously reported that the Suppression Subtractive Hybridization (SSH approach was relevant for the isolation of new mammalian genes involved in oogenesis and early follicle development. Some of these transcripts might be potential new oocyte and granulosa cell markers. We have now characterized one of them, named TOPAZ1 for the Testis and Ovary-specific PAZ domain gene. PRINCIPAL FINDINGS: Sheep and mouse TOPAZ1 mRNA have 4,803 bp and 4,962 bp open reading frames (20 exons, respectively, and encode putative TOPAZ1 proteins containing 1,600 and 1653 amino acids. They possess PAZ and CCCH domains. In sheep, TOPAZ1 mRNA is preferentially expressed in females during fetal life with a peak during prophase I of meiosis, and in males during adulthood. In the mouse, Topaz1 is a germ cell-specific gene. TOPAZ1 protein is highly conserved in vertebrates and specifically expressed in mouse and sheep gonads. It is localized in the cytoplasm of germ cells from the sheep fetal ovary and mouse adult testis. CONCLUSIONS: We have identified a novel PAZ-domain protein that is abundantly expressed in the gonads during germ cell meiosis. The expression pattern of TOPAZ1, and its high degree of conservation, suggests that it may play an important role in germ cell development. Further characterization of TOPAZ1 may elucidate the mechanisms involved in gametogenesis, and particularly in the RNA silencing process in the germ line.

Quantitative expression profile of distinct functional regions in the adult mouse brain.

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Takeya Kasukawa

Full Text Available The adult mammalian brain is composed of distinct regions with specialized roles including regulation of circadian clocks, feeding, sleep/awake, and seasonal rhythms. To find quantitative differences of expression among such various brain regions, we conducted the BrainStars (B* project, in which we profiled the genome-wide expression of ∼50 small brain regions, including sensory centers, and centers for motion, time, memory, fear, and feeding. To avoid confounds from temporal differences in gene expression, we sampled each region every 4 hours for 24 hours, and pooled the samples for DNA-microarray assays. Therefore, we focused on spatial differences in gene expression. We used informatics to identify candidate genes with expression changes showing high or low expression in specific regions. We also identified candidate genes with stable expression across brain regions that can be used as new internal control genes, and ligand-receptor interactions of neurohormones and neurotransmitters. Through these analyses, we found 8,159 multi-state genes, 2,212 regional marker gene candidates for 44 small brain regions, 915 internal control gene candidates, and 23,864 inferred ligand-receptor interactions. We also found that these sets include well-known genes as well as novel candidate genes that might be related to specific functions in brain regions. We used our findings to develop an integrated database (http://brainstars.org/ for exploring genome-wide expression in the adult mouse brain, and have made this database openly accessible. These new resources will help accelerate the functional analysis of the mammalian brain and the elucidation of its regulatory network systems.

In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

Energy Technology Data Exchange (ETDEWEB)

Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.

2006-02-01

The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?

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Fossati, Sara Maria; Candiani, Simona; Nödl, Marie-Therese; Maragliano, Luca; Pennuto, Maria; Domingues, Pedro; Benfenati, Fabio; Pestarino, Mario; Zullo, Letizia

2015-08-01

Acetylcholinesterase (ACHE) is a glycoprotein with a key role in terminating synaptic transmission in cholinergic neurons of both vertebrates and invertebrates. ACHE is also involved in the regulation of cell growth and morphogenesis during embryogenesis and regeneration acting through its non-cholinergic sites. The mollusk Octopus vulgaris provides a powerful model for investigating the mechanisms underlying tissue morphogenesis due to its high regenerative power. Here, we performed a comparative investigation of arm morphogenesis during adult arm regeneration and embryonic arm development which may provide insights on the conserved ACHE pathways. In this study, we cloned and characterized O. vulgaris ACHE, finding a single highly conserved ACHE hydrophobic variant, characterized by prototypical catalytic sites and a putative consensus region for a glycosylphosphatidylinositol (GPI)-anchor attachment at the COOH-terminus. We then show that its expression level is correlated to the stage of morphogenesis in both adult and embryonic arm. In particular, ACHE is localized in typical neuronal sites when adult-like arm morphology is established and in differentiating cell locations during the early stages of arm morphogenesis. This possibility is also supported by the presence in the ACHE sequence and model structure of both cholinergic and non-cholinergic sites. This study provides insights into ACHE conserved roles during processes of arm morphogenesis. In addition, our modeling study offers a solid basis for predicting the interaction of the ACHE domains with pharmacological blockers for in vivo investigations. We therefore suggest ACHE as a target for the regulation of tissue morphogenesis.

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

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Leonardo Maltchik

2012-03-01

Full Text Available 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 (~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 differrent ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region.

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

Science.gov (United States)

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

2012-03-01

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.

Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

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Zarrineh, Peyman; Sánchez-Rodríguez, Aminael; Hosseinkhan, Nazanin; Narimani, Zahra; Marchal, Kathleen; Masoudi-Nejad, Ali

2014-01-01

Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica. PMID:25101984

Reprimo tissue-specific expression pattern is conserved between zebrafish and human.

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Ricardo J Figueroa

Full Text Available Reprimo (RPRM, a member of the RPRM gene family, is a tumor-suppressor gene involved in the regulation of the p53-mediated cell cycle arrest at G2/M. RPRM has been associated with malignant tumor progression and proposed as a potential biomarker for early cancer detection. However, the expression and role of RPRM, as well as its family, are poorly understood and their physiology is as yet unstudied. In this scenario, a model system like the zebrafish could serve to dissect the role of the RPRM family members in vivo. Phylogenetic analysis reveals that RPRM and RPRML have been differentially retained by most species throughout vertebrate evolution, yet RPRM3 has been retained only in a small group of distantly related species, including zebrafish. Herein, we characterized the spatiotemporal expression of RPRM (present in zebrafish as an infraclass duplication rprma/rprmb, RPRML and RPRM3 in the zebrafish. By whole-mount in situ hybridization (WISH and fluorescent in situ hybridization (FISH, we demonstrate that rprm (rprma/rprmb and rprml show a similar spatiotemporal expression profile during zebrafish development. At early developmental stages rprmb is expressed in somites. After one day post-fertilization, rprm (rprma/rprmb and rprml are expressed in the notochord, brain, blood vessels and digestive tube. On the other hand, rprm3 shows the most unique expression profile, being expressed only in the central nervous system (CNS. We assessed the expression patterns of RPRM gene transcripts in adult zebrafish and human RPRM protein product in tissue samples by RT-qPCR and immunohistochemistry (IHC staining, respectively. Strikingly, tissue-specific expression patterns of the RPRM transcripts and protein are conserved between zebrafish and humans. We propose the zebrafish as a powerful tool to elucidate the both physiological and pathological roles of the RPRM gene family.

Anaplasma marginale major surface protein 2 CD4+-T-cell epitopes are evenly distributed in conserved and hypervariable regions (HVR), whereas linear B-cell epitopes are predominantly located in the HVR.

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Abbott, Jeffrey R; Palmer, Guy H; Howard, Chris J; Hope, Jayne C; Brown, Wendy C

2004-12-01

Organisms in the genus Anaplasma express an immunodominant major surface protein 2 (MSP2), composed of a central hypervariable region (HVR) flanked by highly conserved regions. Throughout Anaplasma marginale infection, recombination results in the sequential appearance of novel MSP2 variants and subsequent control of rickettsemia by the immune response, leading to persistent infection. To determine whether immune evasion and selection for variant organisms is associated with a predominant response against HVR epitopes, T-cell and linear B-cell epitopes were localized by measuring peripheral blood gamma interferon-secreting cells, proliferation, and antibody binding to 27 overlapping peptides spanning MSP2 in 16 cattle. Similar numbers of MSP2-specific CD4(+) T-cell epitopes eliciting responses of similar magnitude were found in conserved and hypervariable regions. T-cell epitope clusters recognized by the majority of animals were identified in the HVR (amino acids [aa] 171 to 229) and conserved regions (aa 101 to 170 and 272 to 361). In contrast, linear B-cell epitopes were concentrated in the HVR, residing within hydrophilic sequences. The pattern of recognition of epitope clusters by T cells and of HVR epitopes by B cells is consistent with the influence of protein structure on epitope recognition.

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

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Ando, Amy W.; Mallory, Mindy L.

2012-01-01

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

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.

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Chen, Wen; Zhang, Xuan; Li, Jing; Huang, Shulan; Xiang, Shuanglin; Hu, Xiang; Liu, Changning

2018-05-09

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

Regional differences in gene expression and promoter usage in aged human brains

KAUST Repository

Pardo, Luba M.

2013-02-19

To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites and to quantify the differences in gene expression across the 5 brain regions. We also analyzed the extent to which methylation influenced the observed expression profiles. We sequenced more than 71 million cap analysis of gene expression tags corresponding to 70,202 promoter regions and 16,888 genes. More than 7000 transcripts were differentially expressed, mainly because of differential alternative promoter usage. Unexpectedly, 7% of differentially expressed genes were neurodevelopmental transcription factors. Functional pathway analysis on the differentially expressed genes revealed an overrepresentation of several signaling pathways (e.g., fibroblast growth factor and wnt signaling) in hippocampus and striatum. We also found that although 73% of methylation signals mapped within genes, the influence of methylation on the expression profile was small. Our study underscores alternative promoter usage as an important mechanism for determining the regional differences in gene expression at old age.

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

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Lemay Danielle G

2012-09-01

Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

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

International Nuclear Information System (INIS)

Ledbetter, D.H.; Ledbetter, S.A.; vanTuinen, P.

1989-01-01

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

Economic efficiency and cost implications of habitat conservation: An example in the context of the Edwards Aquifer region

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Gillig, Dhazn; McCarl, Bruce A.; Jones, Lonnie L.; Boadu, Frederick

2004-04-01

Groundwater management in the Edwards Aquifer in Texas is in the process of moving away from a traditional right of capture economic regime toward a more environmentally sensitive scheme designed to preserve endangered species habitats. This study explores economic and environmental implications of proposed groundwater management and water development strategies under a proposed regional Habitat Conservation Plan. Results show that enhancing the habitat by augmenting water flow costs $109-1427 per acre-foot and that regional water development would be accelerated by the more extreme possibilities under the Habitat Conservation Plan. The findings also indicate that a water market would improve regional welfare and lower water development but worsen environmental attributes.

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

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Sinha Amit

2012-06-01

Full Text Available Abstract Background An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans. Results We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance. Conclusion Our data set provides a catalog for future functional investigations and indicates novel insight

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

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Claros M Gonzalo

2010-06-01

Full Text Available Abstract 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

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

Energy Technology Data Exchange (ETDEWEB)

Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

2003-12-31

Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

Global conservation model for a mushy region over a moving substrate

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Kyselica, J.; Šimkanin, J.

2018-03-01

We study solidification over a cool substrate moving with a relative velocity with respect to the rest of the fluid. A mathematical model based on global conservation of solute is presented. The explicit solutions of the governing equations are found and analysed via the asymptotic methods. The assessment of how the boundary-layer flow influences the physical characteristics of the mushy region is given, together with the discussion of a possible connection with the solidification at the inner core boundary.

Plant diversity and conservation status of Himalayan Region Poonch Valley Azad Kashmir (Pakistan).

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Khan, Muhammad Azam; Khan, Mir Ajab; Hussain, Mazhar; Mujtaba, Ghulam

2014-09-01

The plant diversity of Himalayan region has been reduced to greater extent due to environmental degradation and human exploitation. Anthropogenic disturbance was the major factor responsible for fragmentation of forest vegetation into small patches. Little research has been conducted in the Himalayan region of Poonch Valley of North eastern Pakistan with reference to plants biodiversity and its conservation. The present research was carried out to provide a checklist of vegetation for biodiversity conservation. A total of 430 vascular and 5 nonvascular plant species with 5 species of Bryophytes (5 families), 13 species of Pteridophytes (6 families), 4 species of Gymnosperms (1 family) and 413 species of angiosperms (95 families) were enumerated from the Poonch valley Azad Kashmir. The genera were classified into three categories according to the number of species. 25 plant communities with phytosociological parameters and diversity indices were reported. Present study revealed that there were 145 threatened, 30 endangered, 68 vulnerable and 47 rare species. It is recorded that extensive grazing, uprooting of plants and soil slope erosion intensify the environmental problems. Since there is maximum exploitation of vegetation, the valley showed a decline in plant diversity. The study was also indicated that the main threats to the biodiversity are expansion of settlement and army installations in the forest area of the valley. For sustainable use In-situ and Ex-situ conservation, controlled harvesting and afforestation may be the solution. Moreover, forest area should be declared prohibited for settlements and army installations.

Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

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Raherison Elie

2012-08-01

Full Text Available Abstract Background Conifers have very large genomes (13 to 30 Gigabases that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

Regional effects of agricultural conservation practices on nutrient transport

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Anna Maria Garcia; Richard B. Alexander; Jeffrey G. Arnold; Lee Norfleet; Mike White; Dale M. Robertson; Gregory Schwarz

2016-01-01

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 surveyswere compiled to document the adoption of conservation practices. Survey data showed that up to 38...

Regional assessment of the status, distribution and conservation needs of cheetahs in southern Africa

OpenAIRE

Purchase, Gianetta; Marker, Laurie; Marnewick, Kelly; Klein, Rebecca; Williams, Samual

2007-01-01

A country by country assessment of the status, distribution and conservation needs for cheetah Acinonyx jubatus in the southern African region indicates that this area holds a significant proportion of the global population of cheetahs, at least 4 500 adults. The largest proportion of this regional population occurs in four range states, Namibia, Botswana, South Africa and Zimbabwe where it is under threat as a result of conflict with livestock and wildlife ranchers, removal of animals (both ...

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

Science.gov (United States)

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

2013-06-01

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.

Exploring Conservation Options in the Broad-Leaved Korean Pine Mixed Forest of the Changbai Mountain Region

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Lin Ma

2015-05-01

Full Text Available The broad-leaved Korean pine (Pinus koraiensis mixed forest (BKPF is one of the most biodiverse zonal communities in the northern temperate zone. Changbai Mountain in northeastern China contains one of the largest BKPFs in the region. The government of China has established a network of 23 nature reserves to protect the BKPF and the species that depend on it for habitat, including the endangered Siberian tiger (Panthera tigris altaica. This study used the conservation planning software C-Plan to calculate the irreplaceability value of each unit to assess how efficiently and comprehensively the existing conservation network supports biodiversity and to identify gap areas that, if integrated into the network, would expand its protection capability. Results show a number of high-conservation-value planning units concentrated along certain ridges. The existing conservation network is structured such that the habitats of only 24 species (out of a total of 75 achieve established conservation targets. Of the other 51 species, 20 achieve less than 50% of their conservation targets. However, expanding the network to include high-conservation-value gap areas could achieve conservation targets for 64 species and could provide different degrees of protection to the other 11 species. Using C-Plan software can guide decision-making to expand the conservation network in this most precious of mountainous ecological zones.

Species of conservation concern and environmental stressors: Local, regional and global effects [Chapter 6] (Executive Summary)

Science.gov (United States)

Steven M. Ostoja; Matthew L. Brooks; Jeanne C. Chambers; Burton K. Pendleton

2013-01-01

Southern Nevada’s unique landscapes and landforms provide habitat for a diversity of plant and wildlife species of conservation concern including many locally and regionally endemic species. The high population density and urbanization of the Las Vegas metropolitan area is the source of many local and regional stressors that affect these species and their habitats:...

Anterior-posterior regionalized gene expression in the Ciona notochord.

Science.gov (United States)

Reeves, Wendy; Thayer, Rachel; Veeman, Michael

2014-04-01

In the simple ascidian chordate Ciona, the signaling pathways and gene regulatory networks giving rise to initial notochord induction are largely understood and the mechanisms of notochord morphogenesis are being systematically elucidated. The notochord has generally been thought of as a non-compartmentalized or regionalized organ that is not finely patterned at the level of gene expression. Quantitative imaging methods have recently shown, however, that notochord cell size, shape, and behavior vary consistently along the anterior-posterior (AP) axis. Here we screen candidate genes by whole mount in situ hybridization for potential AP asymmetry. We identify 4 genes that show non-uniform expression in the notochord. Ezrin/radixin/moesin (ERM) is expressed more strongly in the secondary notochord lineage than the primary. CTGF is expressed stochastically in a subset of notochord cells. A novel calmodulin-like gene (BCamL) is expressed more strongly at both the anterior and posterior tips of the notochord. A TGF-β ortholog is expressed in a gradient from posterior to anterior. The asymmetries in ERM, BCamL, and TGF-β expression are evident even before the notochord cells have intercalated into a single-file column. We conclude that the Ciona notochord is not a homogeneous tissue but instead shows distinct patterns of regionalized gene expression. Copyright © 2013 Wiley Periodicals, Inc.

Evaluating the impact of water conservation on fate of outdoor water use: a study in an arid region.

Science.gov (United States)

Qaiser, Kamal; Ahmad, Sajjad; Johnson, Walter; Batista, Jacimaria

2011-08-01

In this research, the impact of several water conservation policies and return flow credits on the fate of water used outdoors in an arid region is evaluated using system dynamics modeling approach. Return flow credits is a strategy where flow credits are obtained for treated wastewater returned to a water body, allowing for the withdrawal of additional water equal to the amount returned as treated wastewater. In the return credit strategy, treated wastewater becomes a resource. This strategy creates a conundrum in which conservation may lead to an apparent decrease in water supply because less wastewater is generated and returned to water body. The water system of the arid Las Vegas Valley in Nevada, USA is used as basis for the dynamic model. The model explores various conservation scenarios to attain the daily per capita demand target of 752 l by 2035: (i) status quo situation where conservation is not implemented, (ii) conserving water only on the outdoor side, (iii) conserving water 67% outdoor and 33% indoor, (iv) conserving equal water both in the indoor and outdoor use (v) conserving water only on the indoor side. The model is validated on data from 1993 to 2008 and future simulations are carried out up to 2035. The results show that a substantial portion of the water used outdoor either evapo-transpires (ET) or infiltrates to shallow groundwater (SGW). Sensitivity analysis indicated that seepage to groundwater is more susceptible to ET compared to any other variable. The all outdoor conservation scenario resulted in the highest return flow credits and the least ET and SGW. A major contribution of this paper is in addressing the water management issues that arise when wastewater is considered as a resource and developing appropriate conservation policies in this backdrop. The results obtained can be a guide in developing outdoor water conservation policies in arid regions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Conservation potential of agricultural water conservation subsidies

Science.gov (United States)

Huffaker, Ray

2008-07-01

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

Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus’ molecule 1 protein

International Nuclear Information System (INIS)

Petty, Tom J.; Nishimura, Taisuke; Emamzadah, Soheila; Gabus, Caroline; Paszkowski, Jerzy; Halazonetis, Thanos D.; Thore, Stéphane

2010-01-01

In order to investigate its function in transcriptional gene silencing, the highly conserved motif 2 from A. thaliana Morpheus’ molecule 1 protein was expressed, purified and crystallized. X-ray diffraction analysis is reported to a resolution of 3.2 Å. Of the known epigenetic control regulators found in plants, the Morpheus’ molecule 1 (MOM1) protein is atypical in that the deletion of MOM1 does not affect the level of epigenetic marks controlling the transcriptional status of the genome. A short 197-amino-acid fragment of the MOM1 protein sequence can complement MOM1 deletion when coupled to a nuclear localization signal, suggesting that this region contains a functional domain that compensates for the loss of the full-length protein. Numerous constructs centred on the highly conserved MOM1 motif 2 (CMM2) present in these 197 residues have been generated and expressed in Escherichia coli. Following purification and crystallization screening, diamond-shaped single crystals were obtained that diffracted to ∼3.2 Å resolution. They belonged to the trigonal space group P3 1 21 (or P3 2 21), with unit-cell parameters a = 85.64, c = 292.74 Å. Structure determination is ongoing

Hot Spots and Hot Times: Wildlife Road Mortality in a Regional Conservation Corridor

Science.gov (United States)

Garrah, Evelyn; Danby, Ryan K.; Eberhardt, Ewen; Cunnington, Glenn M.; Mitchell, Scott

2015-10-01

Strategies to reduce wildlife road mortality have become a significant component of many conservation efforts. However, their success depends on knowledge of the temporal and spatial patterns of mortality. We studied these patterns along the 1000 Islands Parkway in Ontario, Canada, a 37 km road that runs adjacent to the St. Lawrence River and bisects the Algonquin-to-Adirondacks international conservation corridor. Characteristics of all vertebrate road kill were recorded during 209 bicycle surveys conducted from 2008 to 2011. We estimate that over 16,700 vertebrates are killed on the road from April to October each year; most are amphibians, but high numbers of birds, mammals, and reptiles were also found, including six reptiles considered at-risk in Canada. Regression tree analysis was used to assess the importance of seasonality, weather, and traffic on road kill magnitude. All taxa except mammals exhibited distinct temporal peaks corresponding to phases in annual life cycles. Variations in weather and traffic were only important outside these peak times. Getis-Ord analysis was used to identify spatial clusters of mortality. Hot spots were found in all years for all taxa, but locations varied annually. A significant spatial association was found between multiyear hot spots and wetlands. The results underscore the notion that multi-species conservation efforts must account for differences in the seasonality of road mortality among species and that multiple years of data are necessary to identify locations where the greatest conservation good can be achieved. This information can be used to inform mitigation strategies with implications for conservation at regional scales.

Conserving the Greater Sage-grouse: A social-ecological systems case study from the California-Nevada region

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Duvall, Alison L; Metcalf, Alexander L.; Coates, Peter S.

2016-01-01

The Endangered Species Act (ESA) continues to serve as one of the most powerful and contested federal legislative mandates for conservation. In the midst of heated debates, researchers, policy makers, and conservation practitioners champion the importance of cooperative conservation and social-ecological systems approaches, which forge partnerships at multiple levels and scales to address complex ecosystem challenges. However, few real-world examples exist to demonstrate how multifaceted collaborations among stakeholders who share a common goal of conserving at-risk species may be nested within a systems framework to achieve social and ecological goals. Here, we present a case study of Greater Sage-grouse (Centrocercus urophasianus) conservation efforts in the “Bi-State” region of California and Nevada, United States. Using key-informant interviews, we explored dimensions and drivers of this landscape-scale conservation effort. Three themes emerged from the interviews, including 1) ESA action was transformed into opportunity for system-wide conservation; 2) a diverse, locally based partnership anchored collaboration and engagement across multiple levels and scales; and 3) best-available science combined with local knowledge led to “certainty of effectiveness and implementation”—the criteria used by the US Fish and Wildlife Service to evaluate conservation efforts when making listing decisions. Ultimately, collaborative conservation through multistakeholder engagement at various levels and scales led to proactive planning and implementation of conservation measures and precluded the need for an ESA listing of the Bi-State population of Greater Sage-grouse. This article presents a potent example of how a systems approach integrating policy, management, and learning can be used to successfully overcome the conflict-laden and “wicked” challenges that surround at-risk species conservation.

Anxa4 Genes are Expressed in Distinct Organ Systems in Xenopus laevis and tropicalis But are Functionally Conserved

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Massé, Karine L; Collins, Robert J; Bhamra, Surinder; Seville, Rachel A

2007-01-01

Anxa4 belongs to the multigenic annexin family of proteins which are characterized by their ability to interact with membranes in a calcium-dependent manner. Defined as a marker for polarized epithelial cells, Anxa4 is believed to be involved in many cellular processes but its functions in vivo are still poorly understood. Previously, we cloned Xanx4 in Xenopus laevis (now referred to as anxa4a) and demonstrated its role during organogenesis of the pronephros, providing the first evidence of a specific function for this protein during the development of a vertebrate. Here, we describe the strict conservation of protein sequence and functional domains of anxa4 during vertebrate evolution. We also identify the paralog of anxa4a, anxa4b and show its specific temporal and spatial expression pattern is different from anxa4a. We show that anxa4 orthologs in X. laevis and tropicalis display expression domains in different organ systems. Whilst the anxa4a gene is mainly expressed in the kidney, Xt anxa4 is expressed in the liver. Finally, we demonstrate Xt anxa4 and anxa4a can display conserved function during kidney organogenesis, despite the fact that Xt anxa4 transcripts are not expressed in this domain. This study highlights the divergence of expression of homologous genes during Xenopus evolution and raises the potential problems of using X. tropicalis promoters in X. laevis. PMID:19279706

Challenges of transfrontier conservation areas: Natural resources nationalism, security and regionalism in the southern African development community region

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Oswell Rusinga

2012-12-01

Full Text Available Transfrontier Conservation Areas (TFCAs initiatives in the Southern African Development Community (SADC region offer hope for providing a mechanism for resolving political tensions and conflicts which are not only related to environmental issues but to security concerns as well. The geopolitical implications of TFCAs in the SADC region cannot be overemphasised with regard to international relations and regional integration. The SADS region is characterised by histories of contested military balance of power and geopolitical rivalries which have a potential to degenerate into military confrontation. Although there is a strong belief in multilateral co-operation among SADC member countries, most of them often engage the international community at the bilateral level. Moreover, there is disharmony in constitutional applications of the rule of law, respect of human rights and good governance. However, TFCAs initiatives in Southern Africa have been seen as offering an opportunity to heal the wounds of pre- and post-independence wars of destabilisation through the encouragement of inter-state collaboration and co-operation by giving governments an opportunity for mutual action on issues of common interest.

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

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

2013-04-01

Fire influences the distribution of fauna in terrestrial biomes throughout the world. Use of fire to achieve a mosaic of vegetation in different stages of succession after burning (i.e., patch-mosaic burning) is a dominant conservation practice in many regions. Despite this, knowledge of how the spatial attributes of vegetation mosaics created by fire affect fauna is extremely scarce, and it is unclear what kind of mosaic land managers should aim to achieve. We selected 28 landscapes (each 12.6 km(2) ) that varied in the spatial extent and diversity of vegetation succession after fire in a 104,000 km(2) area in the semiarid region of southeastern Australia. We surveyed for reptiles at 280 sites nested within the 28 landscapes. The landscape-level occurrence of 9 of the 22 species modeled was associated with the spatial extent of vegetation age classes created by fire. Biogeographic context and the extent of a vegetation type influenced 7 and 4 species, respectively. No species were associated with the diversity of vegetation ages within a landscape. Negative relations between reptile occurrence and both extent of recently burned vegetation (≤10 years postfire, n = 6) and long unburned vegetation (>35 years postfire, n = 4) suggested that a coarse-grained mosaic of areas (e.g. >1000 ha) of midsuccessional vegetation (11-35 years postfire) may support the fire-sensitive reptile species we modeled. This age class coincides with a peak in spinifex cover, a keystone structure for reptiles in semiarid and arid Australia. Maintaining over the long term a coarse-grained mosaic of large areas of midsuccessional vegetation in mallee ecosystems will need to be balanced against the short-term negative effects of large fires on many reptile species and a documented preference by species from other taxonomic groups, particularly birds, for older vegetation. © 2012 Society for Conservation Biology.

Regulation of G-protein coupled receptor traffic by an evolutionary conserved hydrophobic signal.

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Angelotti, Tim; Daunt, David; Shcherbakova, Olga G; Kobilka, Brian; Hurt, Carl M

2010-04-01

Plasma membrane (PM) expression of G-protein coupled receptors (GPCRs) is required for activation by extracellular ligands; however, mechanisms that regulate PM expression of GPCRs are poorly understood. For some GPCRs, such as alpha2c-adrenergic receptors (alpha(2c)-ARs), heterologous expression in non-native cells results in limited PM expression and extensive endoplasmic reticulum (ER) retention. Recently, ER export/retentions signals have been proposed to regulate cellular trafficking of several GPCRs. By utilizing a chimeric alpha(2a)/alpha(2c)-AR strategy, we identified an evolutionary conserved hydrophobic sequence (ALAAALAAAAA) in the extracellular amino terminal region that is responsible in part for alpha(2c)-AR subtype-specific trafficking. To our knowledge, this is the first luminal ER retention signal reported for a GPCR. Removal or disruption of the ER retention signal dramatically increased PM expression and decreased ER retention. Conversely, transplantation of this hydrophobic sequence into alpha(2a)-ARs reduced their PM expression and increased ER retention. This evolutionary conserved hydrophobic trafficking signal within alpha(2c)-ARs serves as a regulator of GPCR trafficking.

Clinicopathologic Significance of Excision Repair Cross-Complementation 1 Expression in Patients Treated With Breast-Conserving Surgery and Radiation Therapy

International Nuclear Information System (INIS)

Goyal, Sharad; Parikh, Rahul R.; Green, Camille; Schiff, Devora B.S.; Moran, Meena S.; Yang Qifeng; Haffty, Bruce G.

2010-01-01

Purpose: The excision repair cross-complementation 1 (ERCC1) enzyme plays a rate-limiting role in the nucleotide excision repair pathway and is associated with resistance to platinum-based chemotherapy in cancers of the head and neck and the lung. The purpose of this study was to evaluate the clinicopathologic and prognostic significance of ERCC1 expression in a cohort of early-stage breast cancer patients treated with breast conservation therapy. Methods and Materials: Paraffin specimens from 504 women with early-stage breast cancer treated with breast conservation therapy were constructed into tissue microarrays. The array was stained for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) and ERCC1. This was then correlated with clinicopathologic factors and outcomes data. Results: ERCC-1 expression was evaluable in 366 cases (72%). In this group, 32% and 38% of patients received adjuvant chemotherapy and hormonal therapy, respectively. Increased ERCC-1 expression was found to be correlated with ER positivity (p 50 (p 50. To our knowledge, this is the first study investigating ERCC1 expression in patients receiving adjuvant radiation therapy for breast cancer.

Evidence for widespread degradation of gene control regions in hominid genomes.

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Peter D Keightley

2005-02-01

Full Text Available Although sequences containing regulatory elements located close to protein-coding genes are often only weakly conserved during evolution, comparisons of rodent genomes have implied that these sequences are subject to some selective constraints. Evolutionary conservation is particularly apparent upstream of coding sequences and in first introns, regions that are enriched for regulatory elements. By comparing the human and chimpanzee genomes, we show here that there is almost no evidence for conservation in these regions in hominids. Furthermore, we show that gene expression is diverging more rapidly in hominids than in murids per unit of neutral sequence divergence. By combining data on polymorphism levels in human noncoding DNA and the corresponding human-chimpanzee divergence, we show that the proportion of adaptive substitutions in these regions in hominids is very low. It therefore seems likely that the lack of conservation and increased rate of gene expression divergence are caused by a reduction in the effectiveness of natural selection against deleterious mutations because of the low effective population sizes of hominids. This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees.

A Useful Expression for Relativistic Energy Conservation of a Point Mass in an Isotropic Static Gravitational Field

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Augousti, A. T.; Radosz, A.; Ostasiewicz, K.

2011-01-01

By using the symmetry and time-independence properties of Schwarzschild spacetime it is demonstrated that an energy conservation law may be expressed in terms of local velocity. From this form three important results may be derived very concisely. This highlights analogies and differences between relativistic and classical approaches to mechanics…

Structural and functional analysis of mouse Msx1 gene promoter: sequence conservation with human MSX1 promoter points at potential regulatory elements.

Science.gov (United States)

Gonzalez, S M; Ferland, L H; Robert, B; Abdelhay, E

1998-06-01

Vertebrate Msx genes are related to one of the most divergent homeobox genes of Drosophila, the muscle segment homeobox (msh) gene, and are expressed in a well-defined pattern at sites of tissue interactions. This pattern of expression is conserved in vertebrates as diverse as quail, zebrafish, and mouse in a range of sites including neural crest, appendages, and craniofacial structures. In the present work, we performed structural and functional analyses in order to identify potential cis-acting elements that may be regulating Msx1 gene expression. To this end, a 4.9-kb segment of the 5'-flanking region was sequenced and analyzed for transcription-factor binding sites. Four regions showing a high concentration of these sites were identified. Transfection assays with fragments of regulatory sequences driving the expression of the bacterial lacZ reporter gene showed that a region of 4 kb upstream of the transcription start site contains positive and negative elements responsible for controlling gene expression. Interestingly, a fragment of 130 bp seems to contain the minimal elements necessary for gene expression, as its removal completely abolishes gene expression in cultured cells. These results are reinforced by comparison of this region with the human Msx1 gene promoter, which shows extensive conservation, including many consensus binding sites, suggesting a regulatory role for them.

Cytoplasmic protein binding to highly conserved sequences in the 3' untranslated region of mouse protamine 2 mRNA, a translationally regulated transcript of male germ cells

International Nuclear Information System (INIS)

Kwon, Y.K.; Hecht, N.B.

1991-01-01

The expression of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated translationally during male germ-cell development. The 3' untranslated region (UTR) of protamine 1 mRNA has been reported to control its time of translation. To understand the mechanisms controlling translation of the protamine mRNAs, we have sought to identify cis elements of the 3' UTR of protamine 2 mRNA that are recognized by cytoplasmic factors. From gel retardation assays, two sequence elements are shown to form specific RNA-protein complexes. Protein binding sites of the two complexes were determined by RNase T1 mapping, by blocking the putative binding sites with antisense oligonucleotides, and by competition assays. The sequences of these elements, located between nucleotides + 537 and + 572 in protamine 2 mRNA, are highly conserved among postmeiotic translationally regulated nuclear proteins of the mammalian testis. Two closely linked protein binding sites were detected. UV-crosslinking studies revealed that a protein of about 18 kDa binds to one of the conserved sequences. These data demonstrate specific protein binding to a highly conserved 3' UTR of translationally regulated testicular mRNA

Deletion of a conserved regulatory element required for Hmx1 expression in craniofacial mesenchyme in the dumbo rat: a newly identified cause of congenital ear malformation

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Lely A. Quina

2012-11-01

Hmx1 is a homeodomain transcription factor expressed in the developing eye, peripheral ganglia, and branchial arches of avian and mammalian embryos. Recent studies have identified a loss-of-function allele at the HMX1 locus as the causative mutation in the oculo-auricular syndrome (OAS in humans, characterized by ear and eye malformations. The mouse dumbo (dmbo mutation, with similar effects on ear and eye development, also results from a loss-of-function mutation in the Hmx1 gene. A recessive dmbo mutation causing ear malformation in rats has been mapped to the chromosomal region containing the Hmx1 gene, but the nature of the causative allele is unknown. Here we show that dumbo rats and mice exhibit similar neonatal ear and eye phenotypes. In midgestation embryos, dumbo rats show a specific loss of Hmx1 expression in neural-crest-derived craniofacial mesenchyme (CM, whereas Hmx1 is expressed normally in retinal progenitors, sensory ganglia and in CM, which is derived from mesoderm. High-throughput resequencing of 1 Mb of rat chromosome 14 from dmbo/dmbo rats, encompassing the Hmx1 locus, reveals numerous divergences from the rat genomic reference sequence, but no coding changes in Hmx1. Fine genetic mapping narrows the dmbo critical region to an interval of ∼410 kb immediately downstream of the Hmx1 transcription unit. Further sequence analysis of this region reveals a 5777-bp deletion located ∼80 kb downstream in dmbo/dmbo rats that is not apparent in 137 other rat strains. The dmbo deletion region contains a highly conserved domain of ∼500 bp, which is a candidate distal enhancer and which exhibits a similar relationship to Hmx genes in all vertebrate species for which data are available. We conclude that the rat dumbo phenotype is likely to result from loss of function of an ultraconserved enhancer specifically regulating Hmx1 expression in neural-crest-derived CM. Dysregulation of Hmx1 expression is thus a candidate mechanism for congenital ear

Passive seismic experiment in the Olduvai Gorge and Laetoli region (Ngorongoro Conservation Area), Northern Tanzania.

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Parisi, Laura; Lombardo, Luigi; Tang, Zheng; Mai, P. Martin

2017-04-01

The Olduvai Gorge and Laetoli basins, located within the Ngorogoro Conservation Area (NCA), are a cornerstone for understanding the evolution of early humans and are two paleo-antropological excavation sites of global importance. NCA is located at the boundary between the Tanzanian Craton and East African Rift (EAR), in the vicinity of Ngorongoro Crater and other major volcanic edifices. Thus, understanding the geology and tectonics of the NCA may shed light onto the question why early Hominins settled in this region. Environmental and geological conditions in the Olduvai and Laetoli region that promoted human settlement and development are still debated by geologists and paleo-anthropologists. Paleo-geographical reconstructions of the study area of the last 2 million years may take advantage of modern passive seismology. Therefore, we installed a dense seismic network covering a surface of approximately 30 x 40 km within the NCA to map the depth extent of known faults, and to identify seismically active faults that have no surface expression. Our ten seismic stations, equipped with Trillium Compact 120 s sensors, started to operate in June 2016 and will continue for a total of 2 years. At the end of the first year, other 5 stations will densify our network. Here we analyse data quality of the first four months of continuous recordings. Our network provides good quality 3-C waveforms in the frequency range of 0.7-50 Hz. Vertical component seismograms record frequencies reliably down to 8 mHz. Preliminary results of the seismicity obtained with standard location procedures show that NCA is characterised by frequent tectonic seismicity (not volcano-related) with Ml between 0.5 and 2.0. Seismic activity is more frequent in the South (Laetoli region) where major fault systems have not been recognised at the surface yet.

Expression of a single siRNA against a conserved region of NP gene strongly inhibits in vitro replication of different Influenza A virus strains of avian and swine origin.

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Stoppani, Elena; Bassi, Ivan; Dotti, Silvia; Lizier, Michela; Ferrari, Maura; Lucchini, Franco

2015-08-01

Influenza A virus is the principal agent responsible of the respiratory tract's infections in humans. Every year, highly pathogenic and infectious strains with new antigenic assets appear, making ineffective vaccines so far developed. The discovery of RNA interference (RNAi) opened the way to the progress of new promising drugs against Influenza A virus and also to the introduction of disease resistance traits in genetically modified animals. In this paper, we show that Madin-Darby Canine Kidney (MDCK) cell line expressing short hairpin RNAs (shRNAs) cassette, designed on a specific conserved region of the nucleoprotein (NP) viral genome, can strongly inhibit the viral replication of four viral strains sharing the target sequence, reducing the viral mRNA respectively to 2.5×10(-4), 7.5×10(-5), 1.7×10(-3), 1.9×10(-4) compared to the control, as assessed by real-time PCR. Moreover, we demonstrate that during the challenge with a viral strain bearing a single mismatch on the target sequence, although a weaker inhibition is observed, viral mRNA is still lowered down to 1.2×10(-3) folds in the shRNA-expressing clone compared to the control, indicating a broad potential use of this approach. In addition, we developed a highly predictive and fast screening test of siRNA sequences based on dual-luciferase assay, useful for the in vitro prediction of the potential effect of viral inhibition. In conclusion, these findings reveal new siRNA sequences able to inhibit Influenza A virus replication and provide a basis for the development of siRNAs as prophylaxis and therapy for influenza infection both in humans and animals. Copyright © 2015 Elsevier B.V. All rights reserved.

A unique genomic sequence in the Wolf-Hirschhorn syndrome [WHS] region of humans is conserved in the great apes.

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Tarzami, S T; Kringstein, A M; Conte, R A; Verma, R S

1996-10-01

The Wolf-Hirschhorn syndrome (WHS) is caused by a partial deletion in the short arm of chromosome 4 band 16.3 (4p 16.3). A unique-sequence human DNA probe (39 kb) localized within this region has been used to search for sequence homology in the apes' equivalent chromosome 3 by FISH-technique. The WHS loci are conserved in higher primates at the expected position. Nevertheless, a control probe, which detects alphoid sequences of the pericentromeric region of humans, is diverged in chimpanzee, gorilla, and orangutan. The conservation of WHS loci and divergence of DNA alphoid sequences have further added to the controversy concerning human descent.

Conservation genetics and genomics of amphibians and reptiles.

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Shaffer, H Bradley; Gidiş, Müge; McCartney-Melstad, Evan; Neal, Kevin M; Oyamaguchi, Hilton M; Tellez, Marisa; Toffelmier, Erin M

2015-01-01

Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

2nd East Africa Regional Workshop Report: Conservation Agriculture in AFRICA - Analysing and Foreseeing its Impact - Comprehending its Adoption

OpenAIRE

Apina, T.; Mkomwa, S.; Mutai, W.; Njeri, A.

2011-01-01

This resource provides a summary of the 2nd East Africa Sub-regional workshop held in Nanyuki, Kenya, on 28-30 March 2011. Attendees included the African Conservation Tillage Network (ACT), Tropical Soil Biology and Fertility Institute (TSBF/AFNET), Agricultural Research for Development (CIRAD), LEIBNIZ-Centre for Agricultural Landscape Research (ZALF), Agricultural Research Institute (ARI) UYOLE, SELIAN Agricultural Research Institute (SARI-MAFC), Conservation Agriculture for Sustainable Agr...

Marketing energy conservation options to Northwest manufactured home buyers

Energy Technology Data Exchange (ETDEWEB)

Hendrickson, P.L.; Mohler, B.L.; Taylor, Z.T.; Lee, A.D.; Onisko, S.A.

1985-06-01

This study relies on extensive, existing survey data and new analyses to develop information that would help design a marketing plan to achieve energy conservation in new manufactured homes. Existing surveys present comprehensive information about regional manufactured home occupants and their homes that are relevant to a potential conservation marketing plan. An independent analysis of the cost-effectiveness of various efficiency improvements provides background information for designing a marketing plan. This analysis focuses on the economic impacts of alternative energy conservation options as perceived by the home owner. Identifying impediments to conservation investments is also very important in designing a marketing plan. A recent report suggests that financial constraints and the need for better information and knowledge about conservation pose the major conservation investment barriers. Since loan interest rates for new manufactured homes typically exceed site-built rates by a considerable amount and the buyers tend to have lower incomes, the economics of manufactured home conservation investments are likely to significantly influence their viability. Conservation information and its presentation directly influences the manufactured home buyer's decision. A marketing plan should address these impediments and their implications very clearly. Dealers express a belief that consumer satisfaction is the major advantage to selling energy efficient manufactured homes. This suggests that targeting dealers in a marketing plan and providing them direct information on consumers' indicated attitudes may be important. 74 refs.

Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers

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Kuzin Alexander

2008-08-01

Full Text Available Abstract Background The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers. Results Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS. Conclusion The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.

Management of the Regional Lymph Nodes Following Breast-Conservation Therapy for Early-Stage Breast Cancer: An Evolving Paradigm

Energy Technology Data Exchange (ETDEWEB)

Warren, Laura E.G. [Harvard Radiation Oncology Program, Boston, Massachusetts (United States); Punglia, Rinaa S.; Wong, Julia S. [Department of Radiation Oncology, Brigham and Women' s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts (United States); Bellon, Jennifer R., E-mail: jbellon@lroc.harvard.edu [Department of Radiation Oncology, Brigham and Women' s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts (United States)

2014-11-15

Radiation therapy to the breast following breast conservation surgery has been the standard of care since randomized trials demonstrated equivalent survival compared to mastectomy and improved local control and survival compared to breast conservation surgery alone. Recent controversies regarding adjuvant radiation therapy have included the potential role of additional radiation to the regional lymph nodes. This review summarizes the evolution of regional nodal management focusing on 2 topics: first, the changing paradigm with regard to surgical evaluation of the axilla; second, the role for regional lymph node irradiation and optimal design of treatment fields. Contemporary data reaffirm prior studies showing that complete axillary dissection may not provide additional benefit relative to sentinel lymph node biopsy in select patient populations. Preliminary data also suggest that directed nodal radiation therapy to the supraclavicular and internal mammary lymph nodes may prove beneficial; publication of several studies are awaited to confirm these results and to help define subgroups with the greatest likelihood of benefit.

Apoptosis and expression of argyrophilic nucleolus organizer regions in epithelial neoplasms of the larynx

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Christiana Vargas Ribeiro

2015-04-01

Full Text Available INTRODUCTION: Occurrence of apoptosis and expression of proliferative markers are powerful tools to establish a prognosis in the follow-up of cancer.OBJECTIVE: To evaluate the growth fraction in papillomas and laryngeal squamous cell carcinomas with three degrees of differentiation through apoptosis and the expression of nucleolus organizer regions.METHODS: Retrospective study from which paraffin material was submitted to microtomy and hematoxylin-eosin and silver staining. Stained slides were used to quantify the apoptotic index and the number of nucleolus organizer regions by morphometry.RESULTS: Apoptosis was significantly more frequent in well differentiated carcinomas and in papillomas, and a higher growth fraction of expressed nucleolus organizer regions and cells that expressed a greater than average number of nucleolus organizer regions were more frequently noted in undifferentiated carcinomas.CONCLUSIONS: Thus, it was possible to verify that a high apoptotic index was associated with a lower chance of tumor differentiation in carcinomas, while a greater number of total nucleolus organizer regions, cells expressing nucleolus organizer regions above average and a higher growth fraction were associated with greater likelihood of abnormal cell proliferation and increased tumor differentiation.

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

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Nikulova, Anna A; Favorov, Alexander V; Sutormin, Roman A; Makeev, Vsevolod J; Mironov, Andrey A

2012-07-01

Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.

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

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Jackson Champer

2016-01-01

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

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

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

2013-08-01

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.

SPECIES DISTRIBUTIONS, SURROGACY, AND IMPORTANT CONSERVATION REGIONS IN CANADA

Science.gov (United States)

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

Recurrent and multiple bladder tumors show conserved expression profiles

International Nuclear Information System (INIS)

Lindgren, David; Fioretos, Thoas; Månsson, Wiking; Höglund, Mattias; Gudjonsson, Sigurdur; Jee, Kowan Ja; Liedberg, Fredrik; Aits, Sonja; Andersson, Anna; Chebil, Gunilla; Borg, Åke; Knuutila, Sakari

2008-01-01

Urothelial carcinomas originate from the epithelial cells of the inner lining of the bladder and may appear as single or as multiple synchronous tumors. Patients with urothelial carcinomas frequently show recurrences after treatment making follow-up necessary. The leading hypothesis explaining the origin of meta- and synchronous tumors assumes a monoclonal origin. However, the genetic relationship among consecutive tumors has been shown to be complex in as much as the genetic evolution does not adhere to the chronological appearance of the metachronous tumors. Consequently, genetically less evolved tumors may appear chronologically later than genetically related but more evolved tumors. Forty-nine meta- or synchronous urothelial tumors from 22 patients were analyzed using expression profiling, conventional CGH, LOH, and mutation analyses. We show by CGH that partial chromosomal losses in the initial tumors may not be present in the recurring tumors, by LOH that different haplotypes may be lost and that detected regions of LOH may be smaller in recurring tumors, and that mutations present in the initial tumor may not be present in the recurring ones. In contrast we show that despite apparent genomic differences, the recurrent and multiple bladder tumors from the same patients display remarkably similar expression profiles. Our findings show that even though the vast majority of the analyzed meta- and synchronous tumors from the same patients are not likely to have originated directly from the preceding tumor they still show remarkably similar expressions profiles. The presented data suggests that an expression profile is established early in tumor development and that this profile is stable and maintained in recurring tumors

Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

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Walker Angela M

2009-04-01

Full Text Available Abstract Background The Pregnancy-associated glycoproteins (PAGs belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1 we performed an in silico analysis of the bovine genome to further characterize the PAG gene family, 2 we scrutinized proximal promoter sequences of the PAG genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3 we determined relative transcript abundance of selected PAGs during pregnancy and, 4 we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, bovine (bo PAG-2. Results From our analysis of the bovine genome, we identified 18 distinct PAG genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all boPAGs. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs, were found to be unique to the modern boPAG grouping, but not the ancient boPAGs. We gathered evidence by means of Q-PCR and screening of EST databases to show that boPAG-2 is the most abundant of all boPAG transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the boPAG-2 gene. Conclusion PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed

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

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Sturm, Nancy R; Dollet, Michel; Lukes, Julius; Campbell, David A

2007-09-01

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 occurring in plants: systemic trypanosomatids multiplying in the sap, those from the laticiferous tubes, and those developing in fruits, seeds or flowers but not in the plant itself and that are frequently considered as opportunistic insect trypanosomatids. As some plant intraphloemic trypanosomatids are the causative agents of important diseases, a clear definition of the different types of trypanosomatids is critical. The conserved region of the mitochondrial minicircle provides several specific features in a small sequence region containing three functionally elements required for minicircle replication. Trees generated from the analysis recapitulated trees drawn from analyses of isoenzymes, RAPD, and particular gene sequences, supporting the validity of the small region used in this work. Three groups of isolates were significant and in accordance with previous work. The peculiarity of phloem-restricted trypanosomatids associated with wilts of coconut and oil palm in Latin America - group H - is confirmed. In agreement with previous studies on their biological and serological properties the results highlighted this group called 'phloemicola'. It always differentiated from all other latex and fruit isolates or opportunistic trypanosomatids, like insect trypanosomatids. We can assert that phloemicola is the only well-defined taxon among all plant trypanosomatids. A group of non-pathogenic latex isolates from South American euphorbs (G), and a heterogenous group (A) including one fruit, one possible latex and one insect isolate are clearly distinct groups. The group of Mediterranean isolates from latex (D), even with a low boostrap, stood out well from other groups. The remainder of the isolates fell into a

Letting Wood Rot: A Case Study on Local Perceptions of Global Conservation Initiatives (Boumba, Niger

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Jocelyn Müller

2011-01-01

Full Text Available Although there is a pressing need for conservation in Africa and a push for such actions to be directed by the community, there is still much conflict both in academia and on the ground regarding the success and methods of community-based conservation. Employing key-informant interviews, focus group discussions and participant observation, we look at how one community has perceived the conservation actions in their village, Boumba, Niger, and the neighbouring national park, Park-W. This study examines local perceptions of the goals, priorities and methods of conservation in Park-W and the Boumba region. We demonstrate that while participants expressed positive alignment with perceived conservation goals, they did not agree with conservation priorities and felt strongly against the methods.  Reframing conservation discourse in the terms of sustainable-use or adaptive management may serve to help translate much of the conservation ethic to local realities. We argue that for local conservation to be culturally sustainable, programmers of conservation must engage the community on their own terms, and recognize the value of local perceptions.

Rewilding the tropics, and other conservation translocations strategies in the tropical Asia-Pacific region

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Louys, Julien; Corlett, Richard T; Price, Gilbert J; Hawkins, Stuart; Piper, Philip J

2014-01-01

Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at-risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large-scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large-scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large-bodied taxa in tropical Asia-Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Energy Technology Data Exchange (ETDEWEB)

Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

2010-07-01

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

Bird Conservation Planning and Implementation in Canada's Intermountain Region

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Ilia Hartasanchez; Krista De Groot; Andre Breault; Rob W. Butler

2005-01-01

Bird conservation planning in British Columbia and Yukon has been carried out by each of the major bird initiatives. The purpose of this paper is to provide a status report of planning activities and to discuss how integration of the initiatives is being accomplished for efficient and effective implementation of bird conservation actions.

Transcriptional activation signals found in the Epstein-Barr virus (EBV) latency C promoter are conserved in the latency C promoter sequences from baboon and Rhesus monkey EBV-like lymphocryptoviruses (cercopithicine herpesviruses 12 and 15).

Science.gov (United States)

Fuentes-Pananá, E M; Swaminathan, S; Ling, P D

1999-01-01

The Epstein-Barr virus (EBV) EBNA2 protein is a transcriptional activator that controls viral latent gene expression and is essential for EBV-driven B-cell immortalization. EBNA2 is expressed from the viral C promoter (Cp) and regulates its own expression by activating Cp through interaction with the cellular DNA binding protein CBF1. Through regulation of Cp and EBNA2 expression, EBV controls the pattern of latent protein expression and the type of latency established. To gain further insight into the important regulatory elements that modulate Cp usage, we isolated and sequenced the Cp regions corresponding to nucleotides 10251 to 11479 of the EBV genome (-1079 to +144 relative to the transcription initiation site) from the EBV-like lymphocryptoviruses found in baboons (herpesvirus papio; HVP) and Rhesus macaques (RhEBV). Sequence comparison of the approximately 1,230-bp Cp regions from these primate viruses revealed that EBV and HVP Cp sequences are 64% conserved, EBV and RhEBV Cp sequences are 66% conserved, and HVP and RhEBV Cp sequences are 65% conserved relative to each other. Approximately 50% of the residues are conserved among all three sequences, yet all three viruses have retained response elements for glucocorticoids, two positionally conserved CCAAT boxes, and positionally conserved TATA boxes. The putative EBNA2 100-bp enhancers within these promoters contain 54 conserved residues, and the binding sites for CBF1 and CBF2 are well conserved. Cp usage in the HVP- and RhEBV-transformed cell lines was detected by S1 nuclease protection analysis. Transient-transfection analysis showed that promoters of both HVP and RhEBV are responsive to EBNA2 and that they bind CBF1 and CBF2 in gel mobility shift assays. These results suggest that similar mechanisms for regulation of latent gene expression are conserved among the EBV-related lymphocryptoviruses found in nonhuman primates.

Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future.

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Sergio A Balaguera-Reina

Full Text Available Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius, defining regional habitat priorities/crocodile conservation units (RHP/CCU and regional research priorities (RRP for this species. We also estimated a species distribution model (SDM to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2 and Venezuela (919 km2, which represents only 10.8% of C. intermedius' potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries. Caño Guaritico (Creek and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species

Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future

Science.gov (United States)

Espinosa-Blanco, Ariel S.; Morales-Betancourt, Mónica A.; Seijas, Andrés E.; Lasso, Carlos A.; Antelo, Rafael; Densmore, Llewellyn D.

2017-01-01

Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius), defining regional habitat priorities/crocodile conservation units (RHP/CCU) and regional research priorities (RRP) for this species. We also estimated a species distribution model (SDM) to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2) and Venezuela (919 km2), which represents only 10.8% of C. intermedius’ potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon) exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries) where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia) and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries). Caño Guaritico (Creek) and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species is

The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2.

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Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

2017-10-03

Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242-596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239-598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848-1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection.

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

KAUST Repository

Seridi, Loqmane

2014-10-07

Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

KAUST Repository

Seridi, Loqmane; Ryu, Tae Woo; Ravasi, Timothy

2014-01-01

Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

Detailed analysis of the δ-crystallin mRNA-expressing region in early development of the chick pituitary gland.

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Inoue, Makiko; Shiina, Tomoya; Aizawa, Sayaka; Sakata, Ichiro; Takagi, Hiroyasu; Sakai, Takafumi

2012-06-01

Although δ-crystallin (δ-crys), also known as lens protein, is transiently expressed in Rathke's pouch (RP) of the chick embryo, detailed temporal and spatial expression patterns have been obscure. In this study, to understand the relationship between the δ-crys mRNA-expressing region and RP formation, we examined the embryonic expression pattern of δ-crys mRNA in the primordium of the adenohypophysis. δ-crys mRNA expression was initially found at stage 15 anterior to the foregut and posterior to the invaginated oral ectoderm. After RP formation, the δ-crys mRNA was expressed in the post-ventral region of RP and the anterior region of RP. δ-crys mRNA expression was then restricted to the cephalic lobe of the pituitary gland. From stage 20, the δ-crys and alpha-glycoprotein subunit (αGSU) mRNA-expressing regions were almost completely overlapping. The αGSU mRNA-expressing region is thought to be the primordium of the pars tuberalis, and these regions were overlapped with the Lhx3 mRNA-expressing region. The intensity of δ-crys mRNA expression gradually decreased with development and completely disappeared by stage 34. These results suggest that the embryonic chick pituitary gland consists of two different regions labeled with δ-crys and Lhx3.

Attitudes of Local People Toward Wildlife Conservation: A Case Study From the Kashmir Valley

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Zaffar Rais Mir

2015-11-01

Full Text Available People’s attitudes toward wildlife conservation can significantly affect the success of conservation initiatives. Understanding the factors influencing these attitudes is essential for designing strategies to alleviate human–wildlife conflict. Although this topic has been studied extensively across diverse regions, there has been no such study in the Kashmir Division of Jammu and Kashmir state, India. We surveyed 3 administrative units around Dachigam National Park through semistructured interviews (n = 384 to investigate the socioeconomic status of local people, the extent of economic damage caused by wild animals, and people’s attitudes toward wildlife conservation. Results, analyzed using a generalized linear model approach, indicated that about 75% of the respondents suffered crop damage, while 23% suffered livestock predation by wild animals. The majority of respondents expressed favorable attitudes toward wildlife, with only about 16% expressing a negative perception. Gender, crop damage, livestock predation, and total livestock holdings were the strongest variables influencing the attitudes of local people in the study area. The study identified the need to use appropriate mitigation measures to minimize economic damage by wildlife in order to reduce negative local attitudes toward wildlife conservation.

In vitro binding of Sorghum bicolor transcription factors ABI4 and ABI5 to a conserved region of a GA 2-OXIDASE promoter: possible role of this interaction in the expression of seed dormancy.

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Cantoro, Renata; Crocco, Carlos Daniel; Benech-Arnold, Roberto Luis; Rodríguez, María Verónica

2013-12-01

The precise adjustment of the timing of dormancy release according to final grain usage is still a challenge for many cereal crops. Grain sorghum [Sorghum bicolor (L.) Moench] shows wide intraspecific variability in dormancy level and susceptibility to pre-harvest sprouting (PHS). Both embryo sensitivity to abscisic acid (ABA) and gibberellin (GA) metabolism play an important role in the expression of dormancy of the developing sorghum grain. In previous works, it was shown that, simultaneously with a greater embryo sensitivity to ABA and higher expression of SbABA-INSENSITIVE 4 (SbABI4) and SbABA-INSENSITIVE 5 (SbABI5), dormant grains accumulate less active GA4 due to a more active GA catabolism. In this work, it is demonstrated that the ABA signalling components SbABI4 and SbABI5 interact in vitro with a fragment of the SbGA 2-OXIDASE 3 (SbGA2ox3) promoter containing an ABA-responsive complex (ABRC). Both transcription factors were able to bind the promoter, although not simultaneously, suggesting that they might compete for the same cis-acting regulatory sequences. A biological role for these interactions in the expression of dormancy of sorghum grains is proposed: either SbABI4 and/or SbABI5 activate transcription of the SbGA2ox3 gene in vivo and promote SbGA2ox3 protein accumulation; this would result in active degradation of GA4, thus preventing germination of dormant grains. A comparative analysis of the 5'-regulatory region of GA2oxs from both monocots and dicots is also presented; conservation of the ABRC in closely related GA2oxs from Brachypodium distachyon and rice suggest that these species might share the same regulatory mechanism as proposed for grain sorghum.

Conservation of targeting but divergence in function and quality control of peroxisomal ABC transporters: an analysis using cross-kingdom expression

NARCIS (Netherlands)

Zhang, Xuebin; de Marcos Lousa, Carine; Schutte-Lensink, Nellie; Ofman, Rob; Wanders, Ronald J.; Baldwin, Stephen A.; Baker, Alison; Kemp, Stephan; Theodoulou, Frederica L.

2011-01-01

ABC (ATP-binding cassette) subfamily D transporters are found in all eukaryotic kingdoms and are known to play essential roles in mammals and plants; however, their number, organization and physiological contexts differ. Via cross-kingdom expression experiments, we have explored the conservation of

Conserved and divergent expression patterns of markers of axial development in reptilian embryos: Chinese soft-shell turtle and Madagascar ground gecko.

Science.gov (United States)

Yoshida, Michio; Kajikawa, Eriko; Kurokawa, Daisuke; Noro, Miyuki; Iwai, Tatsuhiro; Yonemura, Shigenobu; Kobayashi, Kensaku; Kiyonari, Hiroshi; Aizawa, Shinichi

2016-07-01

The processes of development leading up to gastrulation have been markedly altered during the evolution of amniotes, and it is uncertain how the mechanisms of axis formation are conserved and diverged between mouse and chick embryos. To assess the conservation and divergence of these mechanisms, this study examined gene expression patterns during the axis formation process in Chinese soft-shell turtle and Madagascar ground gecko preovipositional embryos. The data suggest that NODAL signaling, similarly to avian embryos but in contrast to eutherian embryos, does not have a role in epiblast and hypoblast development in reptilian embryos. The posterior marginal epiblast (PME) is the initial molecular landmark of axis formation in reptilian embryos prior to primitive plate development. Ontogenetically, PME may be the precursor of the primitive plate, and phylogenetically, Koller's sickle and posterior marginal zone in avian development may have been derived from the PME. Most of the genes expressed in the mouse anterior visceral endoderm (AVE genes), especially signaling antagonist genes, are not expressed in the hypoblast of turtle and gecko embryos, though they are expressed in the avian hypoblast. This study proposes that AVE gene expression in the hypoblast and the visceral endoderm could have been independently established in avian and eutherian lineages, similar to the primitive streak that has been independently acquired in these lineages. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantifying the National Significance of Local Areas for Regional Conservation Planning: North Carolina’s Mountain Treasures

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R. Travis Belote

2017-05-01

Full Text Available Conservation scientists recognize that additional protected areas are needed to maintain biological diversity and ecological processes. As regional conservation planners embark on recommending additional areas for protection in formal ecological reserves, it is important to evaluate candidate lands for their role in building a resilient protected areas system of the future. Here, we evaluate North Carolina’s Mountain Treasures with respect to their (1 ecological integrity, (2 role in connecting existing core protected areas, (3 potential to diversify the ecosystem representation of reserves, and (4 role in maintaining hotspots of biologically-rich areas that are not well protected. Mountain Treasures represent a citizen inventory of roadless areas and serve as candidates for elevated levels of conservation protection on U.S. federal lands. We compared Mountain Treasures to other candidate lands throughout the country to evaluate their potential national significance. While the Mountain Treasures tended to be more impacted by human modifications than other roadless areas, they are as important as other roadless areas with respect to their role in connecting existing protected areas and diversifying representation of ecosystems in conservation reserves. However, Mountain Treasures tended to have a much higher biodiversity priority index than other roadless areas leading to an overall higher composite score compared to other roadless areas. Our analysis serves as an example of how using broad-scale datasets can help conservation planners assess the national significance of local areas.

Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

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Janssen, Ralf

2012-09-01

Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

Conserving Prairie Pothole Region wetlands and surrounding grasslands: evaluating effects on amphibians

Science.gov (United States)

Mushet, David M.; Neau, Jordan L.

2014-01-01

The maintenance of viable and genetically diverse populations of amphibians in the Prairie Pothole Region of the United States depends on upland as well as wetland over-wintering and landscape level habitat features.Prairie pothole wetlands provide important amphibian breeding habitat while grasslands surrounding these wetlands provide foraging habitat for adults, overwintering habitat for some species, and important connectivity among breeding wetlands.Grasslands surrounding wetlands were found to be especially important for wood frogs and northern leopard frogs, while croplands dominated habitat utilized by Great Plains toads and Woodhouse’s toads.Habitat suitability mapping highlighted (1) the influence of deep-water overwintering wetlands on suitable habitat for four of five anuran species encountered; (2) the lack of overlap between areas of core habitat for both the northern leopard frog and wood frog compared to the core habitat for both toad species; and (3) the importance of conservation programs in providing grassland components of northern leopard frog and wood frog habitat.Currently, there are approximately 7.2 million acres (2.9 million hectares, ha) of habitat in the PPR identified as suitable for amphibians. WRP and CRP wetland and grassland habitats accounted for approximately 1.9 million acres (0.75 million ha) or 26 percent of this total area.Continued loss of amphibian habitat resulting from an ongoing trend of returning PPR conservation lands to crop production, will likely have significant negative effects on the region’s ability to maintain amphibian biodiversity. Conversely, increases in conservation wetlands and surrounding grasslands on the PPR landscape have great potential to positively influence the region’s amphibian populations.

Bactericidal activity of M protein conserved region antibodies against group A streptococcal isolates from the Northern Thai population

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Pruksachatkunakorn Chulabhorn

2006-08-01

Full Text Available Abstract Background Most group A streptococcal (GAS vaccine strategies have focused on the surface M protein, a major virulence factor of GAS. The amino-terminus of the M protein elicits antibodies, that are both opsonic and protective, but which are type specific. J14, a chimeric peptide that contains 14 amino acids from the M protein conserved C-region at the carboxy-terminus, offers the possibility of a vaccine which will elicit protective opsonic antibodies against multiple different GAS strains. In this study, we searched for J14 and J14-like sequences and the number of their repeats in the C-region of the M protein from GAS strains isolated from the Northern Thai population. Then, we examined the bactericidal activity of J14, J14.1, J14-R1 and J14-R2 antisera against multiple Thai GAS strains. Results The emm genes of GAS isolates were sequenced and grouped as 14 different J14-types. The most diversity of J14-types was found in the C1-repeat. The J14.1 type was the major sequence in the C2 and C3-repeats. We have shown that antisera raised against the M protein conserved C-repeat region peptides, J14, J14.1, J14-R1 and J14-R2, commonly found in GAS isolates from the Northern Thai population, are able to kill GAS of multiple different emm types derived from an endemic area. The mean percent of bactericidal activities for all J14 and J14-like peptide antisera against GAS isolates were more than 70%. The mean percent of bactericidal activity was highest for J14 antisera followed by J14-R2, J14.1 and J14-R1 antisera. Conclusion Our study demonstrated that antisera raised against the M protein conserved C-repeat region are able to kill multiple different strains of GAS isolated from the Northern Thai population. Therefore, the four conserved "J14" peptides have the potential to be used as GAS vaccine candidates to prevent streptococcal infections in an endemic area.

Conservation businesses and conservation planning in a biological diversity hotspot.

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

2013-08-01

The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

Optimal conservation of migratory species.

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Tara G Martin

Full Text Available BACKGROUND: Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea-regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity bringing into question the utility and efficiency of current conservation efforts. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. CONCLUSIONS/SIGNIFICANCE: We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of

A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression.

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Leonie Alten

Full Text Available The vertebrate organizer and notochord have conserved, essential functions for embryonic development and patterning. The restricted expression of developmental regulators in these tissues is directed by specific cis-regulatory modules (CRMs whose sequence conservation varies considerably. Some CRMs have been conserved throughout vertebrates and likely represent ancestral regulatory networks, while others have diverged beyond recognition but still function over a wide evolutionary range. Here we identify and characterize a mammalian-specific CRM required for node and notochord specific (NNC expression of NOTO, a transcription factor essential for node morphogenesis, nodal cilia movement and establishment of laterality in mouse. A 523 bp enhancer region (NOCE upstream the Noto promoter was necessary and sufficient for NNC expression from the endogenous Noto locus. Three subregions in NOCE together mediated full activity in vivo. Binding sites for known transcription factors in NOCE were functional in vitro but dispensable for NOCE activity in vivo. A FOXA2 site in combination with a novel motif was necessary for NOCE activity in vivo. Strikingly, syntenic regions in non-mammalian vertebrates showed no recognizable sequence similarities. In contrast to its activity in mouse NOCE did not drive NNC expression in transgenic fish. NOCE represents a novel, mammal-specific CRM required for the highly restricted Noto expression in the node and nascent notochord and thus regulates normal node development and function.

A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression.

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Alten, Leonie; Schuster-Gossler, Karin; Eichenlaub, Michael P; Wittbrodt, Beate; Wittbrodt, Joachim; Gossler, Achim

2012-01-01

The vertebrate organizer and notochord have conserved, essential functions for embryonic development and patterning. The restricted expression of developmental regulators in these tissues is directed by specific cis-regulatory modules (CRMs) whose sequence conservation varies considerably. Some CRMs have been conserved throughout vertebrates and likely represent ancestral regulatory networks, while others have diverged beyond recognition but still function over a wide evolutionary range. Here we identify and characterize a mammalian-specific CRM required for node and notochord specific (NNC) expression of NOTO, a transcription factor essential for node morphogenesis, nodal cilia movement and establishment of laterality in mouse. A 523 bp enhancer region (NOCE) upstream the Noto promoter was necessary and sufficient for NNC expression from the endogenous Noto locus. Three subregions in NOCE together mediated full activity in vivo. Binding sites for known transcription factors in NOCE were functional in vitro but dispensable for NOCE activity in vivo. A FOXA2 site in combination with a novel motif was necessary for NOCE activity in vivo. Strikingly, syntenic regions in non-mammalian vertebrates showed no recognizable sequence similarities. In contrast to its activity in mouse NOCE did not drive NNC expression in transgenic fish. NOCE represents a novel, mammal-specific CRM required for the highly restricted Noto expression in the node and nascent notochord and thus regulates normal node development and function.

Notch receptor expression in neurogenic regions of the adult zebrafish brain.

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Vanessa de Oliveira-Carlos

Full Text Available The adult zebrash brain has a remarkable constitutive neurogenic capacity. The regulation and maintenance of its adult neurogenic niches are poorly understood. In mammals, Notch signaling is involved in stem cell maintenance both in embryonic and adult CNS. To better understand how Notch signaling is involved in stem cell maintenance during adult neurogenesis in zebrafish we analysed Notch receptor expression in five neurogenic zones of the adult zebrafish brain. Combining proliferation and glial markers we identified several subsets of Notch receptor expressing cells. We found that 90 [Formula: see text] of proliferating radial glia express notch1a, notch1b and notch3. In contrast, the proliferating non-glial populations of the dorsal telencephalon and hypothalamus rarely express notch3 and about half express notch1a/1b. In the non-proliferating radial glia notch3 is the predominant receptor throughout the brain. In the ventral telencephalon and in the mitotic area of the optic tectum, where cells have neuroepithelial properties, notch1a/1b/3 are expressed in most proliferating cells. However, in the cerebellar niche, although progenitors also have neuroepithelial properties, only notch1a/1b are expressed in a high number of PCNA [Formula: see text] cells. In this region notch3 expression is mostly in Bergmann glia and at low levels in few PCNA [Formula: see text] cells. Additionally, we found that in the proliferation zone of the ventral telencephalon, Notch receptors display an apical high to basal low gradient of expression. Notch receptors are also expressed in subpopulations of oligodendrocytes, neurons and endothelial cells. We suggest that the partial regional heterogeneity observed for Notch expression in progenitor cells might be related to the cellular diversity present in each of these neurogenic niches.

Face-selective regions differ in their ability to classify facial expressions.

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Zhang, Hui; Japee, Shruti; Nolan, Rachel; Chu, Carlton; Liu, Ning; Ungerleider, Leslie G

2016-04-15

Recognition of facial expressions is crucial for effective social interactions. Yet, the extent to which the various face-selective regions in the human brain classify different facial expressions remains unclear. We used functional magnetic resonance imaging (fMRI) and support vector machine pattern classification analysis to determine how well face-selective brain regions are able to decode different categories of facial expression. Subjects participated in a slow event-related fMRI experiment in which they were shown 32 face pictures, portraying four different expressions: neutral, fearful, angry, and happy and belonging to eight different identities. Our results showed that only the amygdala and the posterior superior temporal sulcus (STS) were able to accurately discriminate between these expressions, albeit in different ways: the amygdala discriminated fearful faces from non-fearful faces, whereas STS discriminated neutral from emotional (fearful, angry and happy) faces. In contrast to these findings on the classification of emotional expression, only the fusiform face area (FFA) and anterior inferior temporal cortex (aIT) could discriminate among the various facial identities. Further, the amygdala and STS were better than FFA and aIT at classifying expression, while FFA and aIT were better than the amygdala and STS at classifying identity. Taken together, our findings indicate that the decoding of facial emotion and facial identity occurs in different neural substrates: the amygdala and STS for the former and FFA and aIT for the latter. Published by Elsevier Inc.

Myosin heavy chain expression in cranial, pectoral fin, and tail muscle regions of zebrafish embryos.

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Peng, Mou-Yun; Wen, Hui-Ju; Shih, Li-Jane; Kuo, Ching-Ming; Hwang, Sheng-Ping L

2002-12-01

To investigate whether different myosin heavy chain (MHC) isoforms may constitute myofibrils in the trunk and tail musculature and if their respective expression may be regulated by spadetail (spt) and no tail (brachyury), we identified and characterized mRNA expression patterns of an embryonic- and tail muscle-specific MHC gene (named myhz2) during zebrafish development in wild type, spt, and ntl mutant embryos. The identified myhz2 MHC gene encodes a polypeptide containing 1,935 amino acids. Deduced amino acid comparisons showed that myhz2 MHC shared 92.6% sequence identity with that of carp fast skeletal MHC. Temporal and spatial myhz2 MHC mRNA expression patterns were analyzed by quantitative RT-PCR and whole-mount in situ hybridization using primer pairs and probes designed from the 3'-untranslated region (UTR). Temporally myhz2 MHC mRNA appears in pharyngula embryos and peaks in protruding-mouth larvae. The expression level decreased in 7-day-old hatching larvae, and mRNA expression was not detectable in adult fish. Spatially in pharyngula embryos, mRNA was localized only in the tail somite region, while in long-pec embryos, transcripts were also expressed in the two cranial muscle elements of the adductor mandibulae and medial rectus, as well as in pectoral fin muscles and the tail muscle region. Myhz2 MHC mRNA was expressed in most cranial muscle elements, pectoral fin muscles, and the tail muscle region of 3-day-old hatching larvae. In contrast, no expression of myhz2 MHC mRNA could be observed in spt prim-15 mutant embryos. In spt long-pec mutant embryos, transcripts were expressed in two cranial muscle elements and the tail muscle region, but not in pectoral fin muscles, while only trace amounts of myhz2 MHC mRNA were expressed in the remaining tail muscle region of 38 hpf and long-pec ntl mutant embryos. Copyright 2002 Wiley-Liss, Inc.

Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials

Energy Technology Data Exchange (ETDEWEB)

Fu, Yao, E-mail: Yao.Fu@colorado.edu; Song, Jeong-Hoon, E-mail: JH.Song@colorado.edu

2015-08-01

Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic–continuum bridging.

Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials

International Nuclear Information System (INIS)

Fu, Yao; Song, Jeong-Hoon

2015-01-01

Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic–continuum bridging

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.

Science.gov (United States)

Subramanian, Sankar; Huynen, Leon; Millar, Craig D; Lambert, David M

2010-12-15

Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

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Huynen Leon

2010-12-01

Full Text Available Abstract Background Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

The conservation of Javanese-cultured city through visual expression study on the architecture of Keraton Yogyakarta

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Tohar, Ibrahim; Hardiman, Gagoek; Ratih Sari, Suzanna

2017-12-01

Keraton Yogyakarta as a summit of Javanese culture has been renowned as a heritage building. As object of study, Keraton Yogyakarta is ornamented with a collection of architectural artifacts. The acculturation and merging of these different styles create a unique impression within the palace complex. This study aims to identify the pattern of acculturation of these two styles and to interpret their meaning and expression. A descriptive-qualitative method is employed in this research, which contains visual observation, documentation collection, interviews with informants, and relevant literature review. As results of study, the expression of Tratag Pagelaran, Tratag Sitihinggil, Bangsal Ponconiti, and Gedong Jene tends to widen, while the expression of Gedong Purwaretna tends to uprise. Every building has its own point of interest and ornamentation which its place and content are different.. In visual observations, there are two categories of buildings in Keraton Yogyakarta,which accommodate two styles, namely Javanese Traditional style and Dutch Colonial style. Buildings of Javanese traditional style, which hold a special concept of shading, were built without buttresses and embody a ‘light’ expression, while buildings of Dutch Colonial style, which hold a concept of protection, were built with massive enclosure and produce a “heavy” expression. Although visually split into two distinct styles, the acculturation process in Keraton Yogyakarta produced a unity in its overall expression. The expression pattern of Keraton Yogyakarta can be used as conservation guidance of Javanese-cultured city.

The bioenergy potential of conservation areas and roadsides for biogas in an urbanized region

International Nuclear Information System (INIS)

Van Meerbeek, Koenraad; Ottoy, Sam; De Meyer, Annelies; Van Schaeybroeck, Tom; Van Orshoven, Jos; Muys, Bart; Hermy, Martin

2015-01-01

Highlights: • We assessed the bioenergy potential of conservation areas and roadsides in Flanders. • An area of 31,055 ha produces 203 kton DM of herbaceous biomass annually. • The associated biomass supply chain was optimized with OPTIMASS in four scenarios. • The net energy balance of the studied systems was 7 GJ ha −1 in the 2020 scenarios. • We show that this biomass can play a role to meet the increased biomass demand in 2020. - Abstract: In many urbanized areas the roadside and nature conservation management offers a biomass-for-bioenergy resource potential which is barely valorized, because of the fragmented biomass production sites and the scarcity of accurate data on the spatial availability of the biomass. In this study, a GIS based assessment was performed to determine the regional non-woody biomass-for-bioenergy potential for biogas from conservation areas and roadsides in Flanders, Belgium. These systems, with an area of 31,055 ha, have an annual herbaceous biomass production of 203 kton dry matter. The full associated biomass-to-bioenergy supply chain was optimized in four scenarios to maximize the net energy output and the profit. The scenario analysis was performed with OPTIMASS, a recently developed GIS based strategic decision support system. The analysis showed that the energetic valorization of conservation and roadside biomass through anaerobic digestion had a positive net energy balance, although there is still much room for improvements. Economically, however, it is a less interesting biomass resource. Most likely, the economic picture would change when other ecosystem services delivered by the protected biodiversity would be taken into account. Future technical advances and governmental incentives, like green energy certificates, will be necessary to incorporate the biomass into the energy chain. By tackling the existing barriers and providing a detailed methodology for biomass potential assessments, this study tries to

Nuclear cGMP-dependent kinase regulates gene expression via activity-dependent recruitment of a conserved histone deacetylase complex.

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Yan Hao

2011-05-01

Full Text Available Elevation of the second messenger cGMP by nitric oxide (NO activates the cGMP-dependent protein kinase PKG, which is key in regulating cardiovascular, intestinal, and neuronal functions in mammals. The NO-cGMP-PKG signaling pathway is also a major therapeutic target for cardiovascular and male reproductive diseases. Despite widespread effects of PKG activation, few molecular targets of PKG are known. We study how EGL-4, the Caenorhabditis elegans PKG ortholog, modulates foraging behavior and egg-laying and seeks the downstream effectors of EGL-4 activity. Using a combination of unbiased forward genetic screen and proteomic analysis, we have identified a conserved SAEG-1/SAEG-2/HDA-2 histone deacetylase complex that is specifically recruited by activated nuclear EGL-4. Gene expression profiling by microarrays revealed >40 genes that are sensitive to EGL-4 activity in a SAEG-1-dependent manner. We present evidence that EGL-4 controls egg laying via one of these genes, Y45F10C.2, which encodes a novel protein that is expressed exclusively in the uterine epithelium. Our results indicate that, in addition to cytoplasmic functions, active EGL-4/PKG acts in the nucleus via a conserved Class I histone deacetylase complex to regulate gene expression pertinent to behavioral and physiological responses to cGMP. We also identify transcriptional targets of EGL-4 that carry out discrete components of the physiological response.

Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

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Scharfe Maren

2010-04-01

Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae

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Alexandra Kerbl

2016-08-01

Full Text Available Abstract Background Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain. Despite this heterogeneity of neural arrangements, the molecular profiles related to central nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy. Results We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct-developing meiofaunal annelid Dinophilus gyrociliatus. The small, compact brain shows expression of dimmed, foxg, goosecoid, homeobrain, nk2.1, orthodenticle, orthopedia, pax6, six3/6 and synaptotagmin-1. Although most of the studied markers localize to specific brain areas, the genes six3/6 and synaptotagmin-1 are expressed in nearly all perikarya of the brain. All genes except for goosecoid, pax6 and nk2.2 overlap in the anterior brain region, while the respective expression domains are more separated in the posterior brain. Conclusions Our findings reveal that the expression patterns of the genes foxg, orthodenticle, orthopedia and six3/6 correlate with those described in Platynereis dumerilii larvae, and homeobrain, nk2.1, orthodenticle and synaptotagmin-1 resemble the pattern of late larvae of Capitella teleta. Although data on other annelids are limited, molecular similarities between adult Dinophilus and larval Platynereis and Capitella suggest an overall conservation of molecular mechanisms patterning the anterior neural regions, independent

Regional and temporal differences in gene expression of LH(BETA)T(AG) retinoblastoma tumors.

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Houston, Samuel K; Pina, Yolanda; Clarke, Jennifer; Koru-Sengul, Tulay; Scott, William K; Nathanson, Lubov; Schefler, Amy C; Murray, Timothy G

2011-07-23

The purpose of this study was to evaluate by microarray the hypothesis that LH(BETA)T(AG) retinoblastoma tumors exhibit regional and temporal variations in gene expression. LH(BETA)T(AG) mice aged 12, 16, and 20 weeks were euthanatized (n = 9). Specimens were taken from five tumor areas (apex, anterior lateral, center, base, and posterior lateral). Samples were hybridized to gene microarrays. The data were preprocessed and analyzed, and genes with a P 2.5 were considered to be differentially expressed. Differentially expressed genes were analyzed for overlap with known networks by using pathway analysis tools. There were significant temporal (P regional differences in gene expression for LH(BETA)T(AG) retinoblastoma tumors. At P 2.5, there were significant changes in gene expression of 190 genes apically, 84 genes anterolaterally, 126 genes posteriorly, 56 genes centrally, and 134 genes at the base. Differentially expressed genes overlapped with known networks, with significant involvement in regulation of cellular proliferation and growth, response to oxygen levels and hypoxia, regulation of cellular processes, cellular signaling cascades, and angiogenesis. There are significant temporal and regional variations in the LH(BETA)T(AG) retinoblastoma model. Differentially expressed genes overlap with key pathways that may play pivotal roles in murine retinoblastoma development. These findings suggest the mechanisms involved in tumor growth and progression in murine retinoblastoma tumors and identify pathways for analysis at a functional level, to determine significance in human retinoblastoma. Microarray analysis of LH(BETA)T(AG) retinal tumors showed significant regional and temporal variations in gene expression, including dysregulation of genes involved in hypoxic responses and angiogenesis.

Region-specific expression of mitochondrial complex I genes during murine brain development.

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Stefanie Wirtz

Full Text Available Mutations in the nuclear encoded subunits of mitochondrial complex I (NADH:ubiquinone oxidoreductase may cause circumscribed cerebral lesions ranging from degeneration of the striatal and brainstem gray matter (Leigh syndrome to leukodystrophy. We hypothesized that such pattern of regional pathology might be due to local differences in the dependence on complex I function. Using in situ hybridization we investigated the relative expression of 33 nuclear encoded complex I subunits in different brain regions of the mouse at E11.5, E17.5, P1, P11, P28 and adult (12 weeks. With respect to timing and relative intensity of complex I gene expression we found a highly variant pattern in different regions during development. High average expression levels were detected in periods of intense neurogenesis. In cerebellar Purkinje and in hippocampal CA1/CA3 pyramidal neurons we found a second even higher peak during the period of synaptogenesis and maturation. The extraordinary dependence of these structures on complex I gene expression during synaptogenesis is in accord with our recent findings that gamma oscillations--known to be associated with higher cognitive functions of the mammalian brain--strongly depend on the complex I activity. However, with the exception of the mesencephalon, we detected only average complex I expression levels in the striatum and basal ganglia, which does not explain the exquisite vulnerability of these structures in mitochondrial disorders.

The Neutron-Moisture Meter in Studies of the Effect of Fallow on Water Conservation in Arid Regions

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Oezbek, Nurinnisa; Aksoy, Tevfik; Celebi, Gurkan [Radiophysiology and Soil Fertility Department, Faculty of Agriculture, University of Ankara, Ankara (Turkey)

1967-11-15

For a long time it has been a common practice for the Central Anatolian farmers to leave half the land fallow the whole year in order to increase the amount of water conserved. The main object of these studies was to ascertain whether fallow has an effect on moisture conservation in soils of this region and if so what was its degree of efficiency on a yearly basis. In view of the intensity and distribution of rainfall Ankara, Konya and Eski$ehir were selected for moisture-measurement areas. Altogether 60 holes were dug and 60 access tubes were used for moisture measurements by a neutron- moisture meter, and they were placed at six different locations on either state farms or a dry-farming experimental station. In each location the first group of access tubes were placed in fallow soil, the second in a wheat field and the third in a wheat field after harvest. Each treatment had three replicates. In all holes the moisture measurements were made at five different depths at intervals of either 15 days or one month. At the beginning of the moisture measurements a separate calibration curve was prepared for each location and for each treatment. The measurements were begun in 1964 and are continuing, but with some variations in the sampling technique. Some physical properties of the soils that were sampled from measurement areas, such as texture, field capacity and wilting point, were determined. Some bulk-density measurements were also made by gamma-ray transmission. The results obtained are averaged and illustrated in tables and figures. Necessary calculations and comparisons were made to show the efficiency of the fallow system in the moisture conservation in this dry soil. The results can be summarized as follows: (1) The total amount of water conserved in the soil down to a depth of 1.80 cm was higher in fallow soil than in the other two cases. This was true for all locations over a period of two years. (2) The amounts of water conserved by the effect of fallow

Violations of conservation laws in viscous liquid dynamics

DEFF Research Database (Denmark)

Dyre, Jeppe

2007-01-01

The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover,......, although particle number conservation applies strictly for any liquid, the solidity of viscous liquids implies that even this conservation law is apparently violated in coarse-grained descriptions of density fluctuations.......The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover...

MOUNTAIN NATURAL BIODIVERSITY CONSERVATION IN RUSSIA

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Arkady Tishkov

2012-01-01

Full Text Available High biodiversity and degree of endemism of mountain biota strengthen the mountain regions’ status for the territorial nature conservation. Analysis of the protected areas’ representativeness in various mountain regions of Russia shows some discrepancy between their quantity, square and regional biodiversity originality. The biggest divergences are marked for the Northern Caucasus. The main problems: small area of the protected territories and also cluster character of their spatial distribution, mostly in the high mountains are not supposed to conform with the highest values of the regional flora’s and fauna’s uniqueness, to compensate representativeness of the protected biota and, in anyway, to correspond with the purpose of nature protection frame—the protected territories ecologic network’s forming. The situation in the Urals, Siberia and the Far East seems to be better. The large areas of the protected territories are in general agreement with the high originality of the nature ecosystems. Nevertheless each concrete case needs analysis of the regional biota’s and ecosystems’ biodiversity distribution within the protected areas, including character and (or unique elements of the regional biodiversity to be held. The development of the effectual territorial conservation of mountain regions needs differential approach. The creation of the large representative parcels of nature landscapes in the key-areas has the considerable meaning in the low-developed regions, difficult to access. And well-developed regions have the necessity of nature protected territories’ network development and the planning of the ecological frame’s forming. The territorial biodiversity conservation, including the system of federal, regional and local levels with protective conservation of the rare species has to be combined with ecosystem’s restoration, especially in the zones disturbed by erosion, recreation and military actions. Also it is

Porcine SOX9 Gene Expression Is Influenced by an 18 bp Indel in the 5'-Untranslated Region.

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Bertram Brenig

Full Text Available Sex determining region Y-box 9 (SOX9 is an important regulator of sex and skeletal development and is expressed in a variety of embryonal and adult tissues. Loss or gain of function resulting from mutations within the coding region or chromosomal aberrations of the SOX9 locus lead to a plethora of detrimental phenotypes in humans and animals. One of these phenotypes is the so-called male-to-female or female-to-male sex-reversal which has been observed in several mammals including pig, dog, cat, goat, horse, and deer. In 38,XX sex-reversal French Large White pigs, a genome-wide association study suggested SOX9 as the causal gene, although no functional mutations were identified in affected animals. However, besides others an 18 bp indel had been detected in the 5'-untranslated region of the SOX9 gene by comparing affected animals and controls. We have identified the same indel (Δ18 between position +247 bp and +266 bp downstream the transcription start site of the porcine SOX9 gene in four other pig breeds; i.e., German Large White, Laiwu Black, Bamei, and Erhualian. These animals have been genotyped in an attempt to identify candidate genes for porcine inguinal and/or scrotal hernia. Because the 18 bp segment in the wild type 5'-UTR harbours a highly conserved cAMP-response element (CRE half-site, we analysed its role in SOX9 expression in vitro. Competition and immunodepletion electromobility shift assays demonstrate that the CRE half-site is specifically recognized by CREB. Both binding of CREB to the wild type as well as the absence of the CRE half-site in Δ18 reduced expression efficiency in HEK293T, PK-15, and ATDC5 cells significantly. Transfection experiments of wild type and Δ18 SOX9 promoter luciferase constructs show a significant reduction of RNA and protein levels depending on the presence or absence of the 18 bp segment. Hence, the data presented here demonstrate that the 18 bp indel in the porcine SOX9 5'-UTR is of functional

Are women in the MENA region really that different from women in Europe? Globalization, conservative values and female labor market participation.

OpenAIRE

Fischer, Justina AV; Aydıner-Avşar, Nursel

2015-01-01

This article aims to compare women in the MENA region with women in Europe as to how globalization affects their conservative values and attitudes, and, thereby, their labor market participation. The authors define conservative values as both religious values and socio-political attitudes relating to family issues and leadership. Using micro data from the World Values Survey covering over 80 countries between 1981 and 2014, we employ three distinct indicators of globalization that reflect, fi...

River and wetland classifications for freshwater conservation ...

African Journals Online (AJOL)

River and wetland classifications for freshwater conservation planning in KwaZulu-Natal, South Africa. ... regional- or provincial-scale conservation planning. The hierarchical structure of the classifications provides scope for finer resolution, by the addition of further levels, for application at a sub-regional or municipal scale.

Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region

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Julio Peñas

2016-01-01

Full Text Available Astragalus edulis (Fabaceae is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura. Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.

Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region.

Science.gov (United States)

Peñas, Julio; Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M Montserrat

2016-01-01

Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.

Expression and localization of claudins-3 and -12 in transformed human brain endothelium

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Schrade Anja

2012-02-01

Full Text Available Abstract Background The aim of this study was to characterize the hCMEC/D3 cell line, an in vitro model of the human Blood Brain Barrier (BBB for the expression of brain endothelial specific claudins-3 and -12. Findings hCMEC/D3 cells express claudins-3 and -12. Claudin-3 is distinctly localized to the TJ whereas claudin -12 is observed in the perinuclear region and completely absent from TJs. We show that the expression of both proteins is lost in cell passage numbers where the BBB properties are no longer fully conserved. Expression and localization of claudin-3 is not modulated by simvastatin shown to improve barrier function in vitro and also recommended for routine hCMEC/D3 culture. Conclusions These results support conservation of claudin-3 and -12 expression in the hCMEC/D3 cell line and make claudin-3 a potential marker for BBB characteristics in vitro.

Identification of novel conserved functional motifs across most Influenza A viral strains

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El-Azab Iman

2011-01-01

Full Text Available Abstract Background Influenza A virus poses a continuous threat to global public health. Design of novel universal drugs and vaccine requires a careful analysis of different strains of Influenza A viral genome from diverse hosts and subtypes. We performed a systematic in silico analysis of Influenza A viral segments of all available Influenza A viral strains and subtypes and grouped them based on host, subtype, and years isolated, and through multiple sequence alignments we extrapolated conserved regions, motifs, and accessible regions for functional mapping and annotation. Results Across all species and strains 87 highly conserved regions (conservation percentage > = 90% and 19 functional motifs (conservation percentage = 100% were found in PB2, PB1, PA, NP, M, and NS segments. The conservation percentage of these segments ranged between 94 - 98% in human strains (the most conserved, 85 - 93% in swine strains (the most variable, and 91 - 94% in avian strains. The most conserved segment was different in each host (PB1 for human strains, NS for avian strains, and M for swine strains. Target accessibility prediction yielded 324 accessible regions, with a single stranded probability > 0.5, of which 78 coincided with conserved regions. Some of the interesting annotations in these regions included sites for protein-protein interactions, the RNA binding groove, and the proton ion channel. Conclusions The influenza virus has evolved to adapt to its host through variations in the GC content and conservation percentage of the conserved regions. Nineteen universal conserved functional motifs were discovered, of which some were accessible regions with interesting biological functions. These regions will serve as a foundation for universal drug targets as well as universal vaccine design.

Genome-Wide Expression Profiling of Complex Regional Pain Syndrome

Science.gov (United States)

Jin, Eun-Heui; Zhang, Enji; Ko, Youngkwon; Sim, Woo Seog; Moon, Dong Eon; Yoon, Keon Jung; Hong, Jang Hee; Lee, Won Hyung

2013-01-01

Complex regional pain syndrome (CRPS) is a chronic, progressive, and devastating pain syndrome characterized by spontaneous pain, hyperalgesia, allodynia, altered skin temperature, and motor dysfunction. Although previous gene expression profiling studies have been conducted in animal pain models, there genome-wide expression profiling in the whole blood of CRPS patients has not been reported yet. Here, we successfully identified certain pain-related genes through genome-wide expression profiling in the blood from CRPS patients. We found that 80 genes were differentially expressed between 4 CRPS patients (2 CRPS I and 2 CRPS II) and 5 controls (cut-off value: 1.5-fold change and pCRPS patients and 18 controls by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We focused on the MMP9 gene that, by qRT-PCR, showed a statistically significant difference in expression in CRPS patients compared to controls with the highest relative fold change (4.0±1.23 times and p = 1.4×10−4). The up-regulation of MMP9 gene in the blood may be related to the pain progression in CRPS patients. Our findings, which offer a valuable contribution to the understanding of the differential gene expression in CRPS may help in the understanding of the pathophysiology of CRPS pain progression. PMID:24244504

[Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

Science.gov (United States)

Chakravorty, S; Sarkar, S; Gachhui, R

2015-01-01

The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.

A state-based national network for effective wildlife conservation

Science.gov (United States)

Meretsky, Vicky J.; Maguire, Lynn A.; Davis, Frank W.; Stoms, David M.; Scott, J. Michael; Figg, Dennis; Goble, Dale D.; Griffith, Brad; Henke, Scott E.; Vaughn, Jacqueline; Yaffee, Steven L.

2012-01-01

State wildlife conservation programs provide a strong foundation for biodiversity conservation in the United States, building on state wildlife action plans. However, states may miss the species that are at the most risk at rangewide scales, and threats such as novel diseases and climate change increasingly act at regional and national levels. Regional collaborations among states and their partners have had impressive successes, and several federal programs now incorporate state priorities. However, regional collaborations are uneven across the country, and no national counterpart exists to support efforts at that scale. A national conservation-support program could fill this gap and could work across the conservation community to identify large-scale conservation needs and support efforts to meet them. By providing important information-sharing and capacity-building services, such a program would advance collaborative conservation among the states and their partners, thus increasing both the effectiveness and the efficiency of conservation in the United States.

Costing and Budgeting for Preservation and Conservation in the ...

African Journals Online (AJOL)

Within the Eastern and Southern Africa Regional Branch of the International Council on Archives (ESARBICA) region, little or no information is available on budgeting systems for archival institutions in the region to enhance preservation and conservation programs. Preservation and conservation requires both economic ...

language as a culture and biodiversity conservation

African Journals Online (AJOL)

Guest

biodiversity conservation because life in a particular human environment is ... communication ,by language, by word expression as cultural genes, stories, legends and ..... for expressing individual identity, preserve culture, understanding the ...

RNA-Seq Mouse Brain Regions Expression Data Analysis: Focus on ApoE Functional Network

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Babenko Vladimir N.

2017-09-01

Full Text Available ApoE expression status was proved to be a highly specific marker of energy metabolism rate in the brain. Along with its neighbor, Translocase of Outer Mitochondrial Membrane 40 kDa (TOMM40 which is involved in mitochondrial metabolism, the corresponding genomic region constitutes the neuroenergetic hotspot. Using RNA-Seq data from a murine model of chronic stress a significant positive expression coordination of seven neighboring genes in ApoE locus in five brain regions was observed. ApoE maintains one of the highest absolute expression values genome-wide, implying that ApoE can be the driver of the neighboring gene expression alteration observed under stressful loads. Notably, we revealed the highly statistically significant increase of ApoE expression in the hypothalamus of chronically aggressive (FDR < 0.007 and defeated (FDR < 0.001 mice compared to the control. Correlation analysis revealed a close association of ApoE and proopiomelanocortin (Pomc gene expression profiles implying the putative neuroendocrine stress response background of ApoE expression elevation therein.

Conserved Transcriptional Regulatory Programs Underlying Rice and Barley Germination

Science.gov (United States)

Lin, Li; Tian, Shulan; Kaeppler, Shawn; Liu, Zongrang; An, Yong-Qiang (Charles)

2014-01-01

Germination is a biological process important to plant development and agricultural production. Barley and rice diverged 50 million years ago, but share a similar germination process. To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences. However, BRs with higher protein sequence similarity tended to have more conserved expression patterns. We identified and characterized 316 sets of conserved barley and rice genes (cBRs) with high similarity in both protein sequences and expression patterns, and provided a comprehensive depiction of the transcriptional regulatory program conserved in barley and rice germination at gene, pathway and systems levels. The cBRs encoded proteins involved in a variety of biological pathways and had a wide range of expression patterns. The cBRs encoding key regulatory components in signaling pathways often had diverse expression patterns. Early germination up-regulation of cell wall metabolic pathway and peroxidases, and late germination up-regulation of chromatin structure and remodeling pathways were conserved in both barley and rice. Protein sequence and expression pattern of a gene change quickly if it is not subjected to a functional constraint. Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice. The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence. PMID

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

NARCIS (Netherlands)

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

2005-01-01

The present study evaluated the outcome of salvage treatment for women with local or local-regional recurrence after initial breast conservation treatment with radiation for mammographically detected ductal carcinoma in situ (DCIS; intraductal carcinoma) of the breast. The study cohort consisted of

Replication pattern of the pericentromeric region of chromosome 10q and expression of the RET protooncogene.

Science.gov (United States)

Cinti, R; Schena, F; Passalacqua, M; Ceccherini, I; Ravazzolo, R

2004-08-15

Regulation of the RET gene is highly specific during embryo development and is strictly tissue-specific. Control of transcription depends on mechanisms influenced by epigenetic processes, in particular, histone acetylation at regions flanking the 5' end of the gene. Since the RET gene is mapped in the pericentromeric region of the human chromosome 10, the implication of epigenetic processes is even more striking and worth to be investigated in an extended chromosomal tract. One experimental approach to study the chromatin status in relationship with gene transcription is to assess the replication timing, which we did by using fluorescent in situ hybridization in cells expressing or not expressing the RET gene. By using probes spanning a 700-kb genomic region from the RET locus toward the centromere, we found a relationship between RET expression and early replication. Different patterns were observed between cells naturally expressing RET and cells induced to expression of RET by treatment with sodium butyrate, an inhibitor of histone deacetylases. Three-dimensional analysis of the nuclear localization of fluorescent signals by confocal microscopy showed difference of localization between the RET probe and a probe for a housekeeping gene, G3PDH, located at 12p13.3, in cells that do not express RET, in accordance with previous data for other genes and chromosomal regions. However, RET-expressing cells showed a localization of signals which was not consistent with that expected for expressed genes.

Identification of a set of genes showing regionally enriched expression in the mouse brain

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Marra Marco A

2008-07-01

Full Text Available Abstract Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters ( Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

DEFF Research Database (Denmark)

Olsen, Lars Rønn; Simon, Christian; Kudahl, Ulrich J.

2015-01-01

Background: Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte antigen molecules. However, experimental studies have shown that T cells often...... target diverse regions in highly variable viral pathogens and this diversity may need to be addressed through redefinition of suitable peptide targets. Methods: We have developed a method for antigen assessment and target selection for polyvalent vaccines, with which we identified immune epitopes from...... variable regions, where all variants bind HLA. These regions, although variable, can thus be considered stable in terms of HLA binding and represent valuable vaccine targets. Results: We applied this method to predict CD8+ T-cell targets in influenza A H7N9 hemagglutinin and significantly increased...

A national geographic framework for guiding conservation on a landscape scale

Science.gov (United States)

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

2012-01-01

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

Asymptotic Conservation Laws in Classical Field Theory

International Nuclear Information System (INIS)

Anderson, I.M.; Torre, C.G.

1996-01-01

A new, general, field theoretic approach to the derivation of asymptotic conservation laws is presented. In this approach asymptotic conservation laws are constructed directly from the field equations according to a universal prescription which does not rely upon the existence of Noether identities or any Lagrangian or Hamiltonian formalisms. The resulting general expressions of the conservation laws enjoy important invariance properties and synthesize all known asymptotic conservation laws, such as the Arnowitt-Deser-Misner energy in general relativity. copyright 1996 The American Physical Society

Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion

Science.gov (United States)

Tan, Chunjian; Cao, Xue; Yuan, Shuai; Wang, Weiyu; Feng, Yongzhong; Qiao, Bo

2015-12-01

Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrients in soils subjected to non-traditional tillage treatments decreased during the first several years and then remained stable over the last several years of the experiment. The soil organic matter and total nitrogen content increased gradually over 6 years in all treatments except CK. The nutrient content of soils subjected to conservative tillage methods, such as NT and SM, were significantly higher than those in soils under the CK treatment. Straw mulching and film mulching effectively reduced an observed decrease in soybean yield. Over the final 6 years of the experiment, soybean yields followed the trend RPM > PM > SM > NT > CK > In. This trend has implications for controlling soil erosion and preventing non-point source pollution in sloping fields by sacrificing some food production.

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

Science.gov (United States)

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

2014-01-01

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

Smart spatial incentives for market-based conservation

OpenAIRE

Hartig, Florian; Drechsler, Martin

2008-01-01

Market-based instruments such as payments, auctions or tradable permits have been proposed as flexible and cost-effective instruments for biodiversity conservation on private lands. Trading the service of conservation requires one to define a metric that determines the extent to which a conserved site adds to the regional conservation objective. Yet, while markets for conservation are widely discussed and increasingly applied, little research has been conducted on explicitly accounting for sp...

Global mapping of ecosystem services and conservation priorities

Science.gov (United States)

Naidoo, R.; Balmford, A.; Costanza, R.; Fisher, B.; Green, R. E.; Lehner, B.; Malcolm, T. R.; Ricketts, T. H.

2008-01-01

Global efforts to conserve biodiversity have the potential to deliver economic benefits to people (i.e., “ecosystem services”). However, regions for which conservation benefits both biodiversity and ecosystem services cannot be identified unless ecosystem services can be quantified and valued and their areas of production mapped. Here we review the theory, data, and analyses needed to produce such maps and find that data availability allows us to quantify imperfect global proxies for only four ecosystem services. Using this incomplete set as an illustration, we compare ecosystem service maps with the global distributions of conventional targets for biodiversity conservation. Our preliminary results show that regions selected to maximize biodiversity provide no more ecosystem services than regions chosen randomly. Furthermore, spatial concordance among different services, and between ecosystem services and established conservation priorities, varies widely. Despite this lack of general concordance, “win–win” areas—regions important for both ecosystem services and biodiversity—can be usefully identified, both among ecoregions and at finer scales within them. An ambitious interdisciplinary research effort is needed to move beyond these preliminary and illustrative analyses to fully assess synergies and trade-offs in conserving biodiversity and ecosystem services. PMID:18621701

Molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer myostatin gene

Directory of Open Access Journals (Sweden)

Smith-Keune Carolyn

2008-02-01

Full Text Available Abstract Background Myostatin (MSTN is a member of the transforming growth factor-β superfamily that negatively regulates growth of skeletal muscle tissue. The gene encoding for the MSTN peptide is a consolidate candidate for the enhancement of productivity in terrestrial livestock. This gene potentially represents an important target for growth improvement of cultured finfish. Results Here we report molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer MSTN-1 gene. The barramundi MSTN-1 was encoded by three exons 379, 371 and 381 bp in length and translated into a 376-amino acid peptide. Intron 1 and 2 were 412 and 819 bp in length and presented typical GT...AG splicing sites. The upstream region contained cis-regulatory elements such as TATA-box and E-boxes. A first assessment of sequence variability suggested that higher mutation rates are found in the 5' flanking region with several SNP's present in this species. A putative micro RNA target site has also been observed in the 3'UTR (untranslated region and is highly conserved across teleost fish. The deduced amino acid sequence was conserved across vertebrates and exhibited characteristic conserved putative functional residues including a cleavage motif of proteolysis (RXXR, nine cysteines and two glycosilation sites. A qualitative analysis of the barramundi MSTN-1 expression pattern revealed that, in adult fish, transcripts are differentially expressed in various tissues other than skeletal muscles including gill, heart, kidney, intestine, liver, spleen, eye, gonad and brain. Conclusion Our findings provide valuable insights such as sequence variation and genomic information which will aid the further investigation of the barramundi MSTN-1 gene in association with growth. The finding for the first time in finfish MSTN of a miRNA target site in the 3'UTR provides an opportunity for the identification of regulatory mutations on the

Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii).

Science.gov (United States)

Yeaman, Sam; Hodgins, Kathryn A; Suren, Haktan; Nurkowski, Kristin A; Rieseberg, Loren H; Holliday, Jason A; Aitken, Sally N

2014-07-01

Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Modeling the impact of future development and public conservation orientation on landscape connectivity for conservation planning

DEFF Research Database (Denmark)

Lechner, Alex Mark; Brown, Greg; Raymond, Christopher Mark

2015-01-01

aspects of conservation planning. Objectives We present an approach for characterizing the potential effects of public conservation orientation and projected future development land use scenarios on landscape connectivity. Methods Using public participation GIS techniques (mail-based surveys linked...... to a mapping component), we classified spatially explicit conservation values and preferences into a conservation orientation index consisting of positive, negative, or neutral scores. Connectivity was then modeled using a least-cost path and graph-network approach for a range of conservation orientation...... and development scenarios in the Lower Hunter region, Australia. Scenarios were modelled through either adding vegetation (positive orientation) or removing vegetation (negative orientation, development). Results Scenarios that included positive conservation orientation link the isolated eastern and western...

Growth and gene expression are predominantly controlled by distinct regions of the human IL-4 receptor.

Science.gov (United States)

Ryan, J J; McReynolds, L J; Keegan, A; Wang, L H; Garfein, E; Rothman, P; Nelms, K; Paul, W E

1996-02-01

IL-4 causes hematopoietic cells to proliferate and express a series of genes, including CD23. We examined whether IL-4-mediated growth, as measured by 4PS phosphorylation, and gene induction were similarly controlled. Studies of M12.4.1 cells expressing human IL-4R truncation mutants indicated that the region between amino acids 557-657 is necessary for full gene expression, which correlated with Stat6 DNA binding activity. This region was not required for 4PS phosphorylation. Tyrosine-to-phenylalanine mutations in the interval between amino acids 557-657 revealed that as long as one tyrosine remained unmutated, CD23 was fully induced. When all three tyrosines were mutated, the receptor was unable to induce CD23. The results indicate that growth regulation and gene expression are principally controlled by distinct regions of IL-4R.

Structure and expression of MHC class Ib genes of the central M region in rat and mouse: M4, M5, and M6.

Science.gov (United States)

Lambracht-Washington, Doris; Moore, Yuki F; Wonigeit, Kurt; Lindahl, Kirsten Fischer

2008-04-01

The M region at the telomeric end of the murine major histocompatibility complex (MHC) contains class I genes that are highly conserved in rat and mouse. We have sequenced a cosmid clone of the LEW rat strain (RT1 haplotype) containing three class I genes, RT1.M6-1, RT1.M4, and RT1.M5. The sequences of allelic genes of the BN strain (RT1n haplotype) were obtained either from cDNAs or genomic clones. For the coding parts of the genes few differences were found between the two RT1 haplotypes. In LEW, however, only RT1.M5 and RT1.M6 have open reading frames; whereas in BN all three genes were intact. In line with the findings in BN, transcription was found for all three rat genes in several tissues from strain Sprague Dawley. Protein expression in transfectants could be demonstrated for RT1.M6-1 using the monoclonal antibody OX18. By sequencing of transcripts obtained by RT-PCR, a second, transcribed M6 gene, RT1.M6-2, was discovered, which maps next to RT1.M6-1 outside of the region covered by the cosmid. In addition, alternatively spliced forms for RT1.M5 and RT1.M6 were detected. Of the orthologous mouse genes, H2-M4, H2-M5, and H2-M6, only H2-M5 has an open reading frame. Other important differences between the corresponding parts of the M region of the two species are insertion of long LINE repeats, duplication of RT1.M6, and the inversion of RT1.M5 in the rat. This demonstrates substantial evolutionary dynamics in this region despite conservation of the class I gene sequences themselves.

Human developmental enhancers conserved between deuterostomes and protostomes.

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Shoa L Clarke

Full Text Available The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores. Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.

Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

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Blakely, Collin M; Stoddard, Alexander J; Belka, George K; Dugan, Katherine D; Notarfrancesco, Kathleen L; Moody, Susan E; D'Cruz, Celina M; Chodosh, Lewis A

2006-06-15

Women who have their first child early in life have a substantially lower lifetime risk of breast cancer. The mechanism for this is unknown. Similar to humans, rats exhibit parity-induced protection against mammary tumorigenesis. To explore the basis for this phenomenon, we identified persistent pregnancy-induced changes in mammary gene expression that are tightly associated with protection against tumorigenesis in multiple inbred rat strains. Four inbred rat strains that exhibit marked differences in their intrinsic susceptibilities to carcinogen-induced mammary tumorigenesis were each shown to display significant protection against methylnitrosourea-induced mammary tumorigenesis following treatment with pregnancy levels of estradiol and progesterone. Microarray expression profiling of parous and nulliparous mammary tissue from these four strains yielded a common 70-gene signature. Examination of the genes constituting this signature implicated alterations in transforming growth factor-beta signaling, the extracellular matrix, amphiregulin expression, and the growth hormone/insulin-like growth factor I axis in pregnancy-induced alterations in breast cancer risk. Notably, related molecular changes have been associated with decreased mammographic density, which itself is strongly associated with decreased breast cancer risk. Our findings show that hormone-induced protection against mammary tumorigenesis is widely conserved among divergent rat strains and define a gene expression signature that is tightly correlated with reduced mammary tumor susceptibility as a consequence of a normal developmental event. Given the conservation of this signature, these pathways may contribute to pregnancy-induced protection against breast cancer.

Expression of Tau Pathology-Related Proteins in Different Brain Regions: A Molecular Basis of Tau Pathogenesis.

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Hu, Wen; Wu, Feng; Zhang, Yanchong; Gong, Cheng-Xin; Iqbal, Khalid; Liu, Fei

2017-01-01

Microtubule-associated protein tau is hyperphosphorylated and aggregated in affected neurons in Alzheimer disease (AD) brains. The tau pathology starts from the entorhinal cortex (EC), spreads to the hippocampus and frontal and temporal cortices, and finally to all isocortex areas, but the cerebellum is spared from tau lesions. The molecular basis of differential vulnerability of different brain regions to tau pathology is not understood. In the present study, we analyzed brain regional expressions of tau and tau pathology-related proteins. We found that tau was hyperphosphorylated at multiple sites in the frontal cortex (FC), but not in the cerebellum, from AD brain. The level of tau expression in the cerebellum was about 1/4 of that seen in the frontal and temporal cortices in human brain. In the rat brain, the expression level of tau with three microtubule-binding repeats (3R-tau) was comparable in the hippocampus, EC, FC, parietal-temporal cortex (PTC), occipital-temporal cortex (OTC), striatum, thalamus, olfactory bulb (OB) and cerebellum. However, the expression level of 4R-tau was the highest in the EC and the lowest in the cerebellum. Tau phosphatases, kinases, microtubule-related proteins and other tau pathology-related proteins were also expressed in a region-specific manner in the rat brain. These results suggest that higher levels of tau and tau kinases in the EC and low levels of these proteins in the cerebellum may accounts for the vulnerability and resistance of these representative brain regions to the development of tau pathology, respectively. The present study provides the regional expression profiles of tau and tau pathology-related proteins in the brain, which may help understand the brain regional vulnerability to tau pathology in neurodegenerative tauopathies.

GIS Data Modeling of a Regional Geological Structure by Integrating Geometric and Semantic Expressions

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HE Handong

2017-08-01

Full Text Available Using GIS, data models of geology via geometric descriptions and expressions are being developed. However, the role played by these data models in terms of the description and expression of geological structure phenomenon is limited. To improve the semantic information in geological GIS data models, this study adopts an object-oriented method that describes and expresses the geometric and semantic features of the geological structure phenomenon using geological objects and designs a data model of regional geological structures by integrating geometry and semantics. Moreover, the study designs a semantic "vocabulary-explanation-graph" method for describing the geological phenomenon of structures. Based on the semantic features of regional geological structures and a linear classification method, it divides the regional geological structure phenomenon into 3 divisions, 10 groups, 33 classes and defines the element set and element class. Moreover, it builds the basic geometric network for geological elements based on the geometric and semantic relations among geological objects. Using the ArcGIS Diagrammer Geodatabase, it considers the regional geological structure of the Ning-Zhen Mountains to verify the data model, and the results indicate a high practicability.

Many-body current formula and current conservation for non-equilibrium fully interacting nanojunctions

International Nuclear Information System (INIS)

Ness, H; Dash, L K

2012-01-01

We consider the electron transport properties through fully interacting nanoscale junctions beyond the linear-response regime. We calculate the current flowing through an interacting region connected to two interacting leads, with interaction crossing at the left and right contacts, by using a non-equilibrium Green function technique. The total current at one interface (the left one for example) is made of several terms which can be regrouped into two sets. The first set corresponds to a very generalized Landauer-like current formula with physical quantities defined only in the interacting central region and with renormalized lead self-energies. The second set characterizes inelastic scattering events occurring in the left lead. We show how this term can be negligible or even vanish due to the pseudo-equilibrium statistical properties of the lead in the thermodynamic limit. The expressions for the different Green functions needed for practical calculations of the current are also provided. We determine the constraints imposed by the physical condition of current conservation. The corresponding equation imposed on the different self-energy quantities arising from the current conservation is derived. We discuss in detail its physical interpretation and its relation with previously derived expressions. Finally several important key features are discussed in relation to the implementation of our formalism for calculations of quantum transport in realistic systems. (paper)

Conservation challenges for the Austral and Neotropical America section.

Science.gov (United States)

Ceballos, Gerardo; Vale, Mariana M; Bonacic, Cristian; Calvo-Alvarado, Julio; List, Rurik; Bynum, Nora; Medellín, Rodrigo A; Simonetti, Javier A; Rodríguez, Jon Paul

2009-08-01

The Austral and Neotropical America (ANA) section of the Society for Conservation Biology includes a vast territory with some of the largest relatively pristine ecosystems in the world. With more than 573 million people, the economic growth of the region still depends strongly on natural resource exploitation and still has high rates of environmental degradation and biodiversity loss. A survey among the ANA section membership, with more than 700 members, including most of the section's prominent ecologists and conservationists, indicates that lack of capacity building for conservation, corruption, and threats such as deforestation and illegal trade of species, are among the most urgent problems that need to be addressed to improve conservation in the region. There are, however, strong universities and ecology groups taking the lead in environmental research and conservation, a most important issue to enhance the ability of the region to solve conservation and development conflicts.

Fine-resolution conservation planning with limited climate-change information.

Science.gov (United States)

Shah, Payal; Mallory, Mindy L; Ando, Amy W; Guntenspergen, Glenn R

2017-04-01

Climate-change induced uncertainties in future spatial patterns of conservation-related outcomes make it difficult to implement standard conservation-planning paradigms. A recent study translates Markowitz's risk-diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate-change scenarios for carrying out fine-resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk-return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate-change information and full climate-change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate-change forecasts such that the best possible risk-return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate-change information could be reduced by 17% relative to other iterative approaches. © 2016 Society for Conservation Biology.

Conserving and managing the subnivium.

Science.gov (United States)

Zuckerberg, Benjamin; Pauli, Jonathan N

2018-02-08

In regions where snowfall historically has been a defining seasonal characteristic of the landscape, warming winters have reduced the depth, duration, and extent of snowpack. However, most management and conservation has focused on how aboveground wildlife will be affected by altered snow conditions, even though the majority of species that persist through the winter do so under the snowpack in a thermally stable refugium: the subnivium. Shortened winters, forest management practices, and winter recreation can alter subnivium conditions by increasing snow compaction and compromising thermal stability at the soil-snow interface. To help slow the loss of the subnivium in the face of rapidly changing winter conditions, we suggest managers adopt regional conservation plans for identifying threatened snow-covered environments; measure and predict the effects land cover and habitat management has on local subnivium conditions; and control the timing and distribution of activities that disturb and compact snow cover (e.g., silvicultural practices, snow recreation, and road and trail maintenance). As a case study, we developed a spatially explicit model of subnivium presence in a working landscape of the Chequamegon National Forest, Wisconsin. We identified landscapes where winter recreation and management practices could threaten potentially important areas for subnivium persistence. Similar modeling approaches could inform management decisions related to subnivium conservation. Current climate projections predict that snow seasons will change rapidly in many regions, and as result, we advocate for the immediate recognition, conservation, and management of the subnivium and its dependent species. © 2018 Society for Conservation Biology.

Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization.

Science.gov (United States)

Yang, Guanghui; Liu, Zhenshan; Gao, Lulu; Yu, Kuohai; Feng, Man; Yao, Yingyin; Peng, Huiru; Hu, Zhaorong; Sun, Qixin; Ni, Zhongfu; Xin, Mingming

2018-01-01

Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent of origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid ( Aegilops spp), tetraploid, and hexaploid wheat ( Triticum spp) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene Ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Nearly half of the imprinted genes exhibited conserved expression patterns during wheat hexaploidization. In addition, 40% of the homoeolog pairs originating from whole-genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. These results suggest that genomic imprinting was evolutionarily conserved between closely related Triticum and Aegilops species and in the face of polyploid hybridization between species in these genera. © 2018 American Society of Plant Biologists. All rights reserved.

Brain region-specific expression of MeCP2 isoforms correlates with DNA methylation within Mecp2 regulatory elements.

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Carl O Olson

Full Text Available MeCP2 is a critical epigenetic regulator in brain and its abnormal expression or compromised function leads to a spectrum of neurological disorders including Rett Syndrome and autism. Altered expression of the two MeCP2 isoforms, MeCP2E1 and MeCP2E2 has been implicated in neurological complications. However, expression, regulation and functions of the two isoforms are largely uncharacterized. Previously, we showed the role of MeCP2E1 in neuronal maturation and reported MeCP2E1 as the major protein isoform in the adult mouse brain, embryonic neurons and astrocytes. Recently, we showed that DNA methylation at the regulatory elements (REs within the Mecp2 promoter and intron 1 impact the expression of Mecp2 isoforms in differentiating neural stem cells. This current study is aimed for a comparative analysis of temporal, regional and cell type-specific expression of MeCP2 isoforms in the developing and adult mouse brain. MeCP2E2 displayed a later expression onset than MeCP2E1 during mouse brain development. In the adult female and male brain hippocampus, both MeCP2 isoforms were detected in neurons, astrocytes and oligodendrocytes. Furthermore, MeCP2E1 expression was relatively uniform in different brain regions (olfactory bulb, striatum, cortex, hippocampus, thalamus, brainstem and cerebellum, whereas MeCP2E2 showed differential enrichment in these brain regions. Both MeCP2 isoforms showed relatively similar distribution in these brain regions, except for cerebellum. Lastly, a preferential correlation was observed between DNA methylation at specific CpG dinucleotides within the REs and Mecp2 isoform-specific expression in these brain regions. Taken together, we show that MeCP2 isoforms display differential expression patterns during brain development and in adult mouse brain regions. DNA methylation patterns at the Mecp2 REs may impact this differential expression of Mecp2/MeCP2 isoforms in brain regions. Our results significantly contribute

Genome-wide expression profiling of complex regional pain syndrome.

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Eun-Heui Jin

Full Text Available Complex regional pain syndrome (CRPS is a chronic, progressive, and devastating pain syndrome characterized by spontaneous pain, hyperalgesia, allodynia, altered skin temperature, and motor dysfunction. Although previous gene expression profiling studies have been conducted in animal pain models, there genome-wide expression profiling in the whole blood of CRPS patients has not been reported yet. Here, we successfully identified certain pain-related genes through genome-wide expression profiling in the blood from CRPS patients. We found that 80 genes were differentially expressed between 4 CRPS patients (2 CRPS I and 2 CRPS II and 5 controls (cut-off value: 1.5-fold change and p<0.05. Most of those genes were associated with signal transduction, developmental processes, cell structure and motility, and immunity and defense. The expression levels of major histocompatibility complex class I A subtype (HLA-A29.1, matrix metalloproteinase 9 (MMP9, alanine aminopeptidase N (ANPEP, l-histidine decarboxylase (HDC, granulocyte colony-stimulating factor 3 receptor (G-CSF3R, and signal transducer and activator of transcription 3 (STAT3 genes selected from the microarray were confirmed in 24 CRPS patients and 18 controls by quantitative reverse transcription-polymerase chain reaction (qRT-PCR. We focused on the MMP9 gene that, by qRT-PCR, showed a statistically significant difference in expression in CRPS patients compared to controls with the highest relative fold change (4.0±1.23 times and p = 1.4×10(-4. The up-regulation of MMP9 gene in the blood may be related to the pain progression in CRPS patients. Our findings, which offer a valuable contribution to the understanding of the differential gene expression in CRPS may help in the understanding of the pathophysiology of CRPS pain progression.

MAPT expression and splicing is differentially regulated by brain region: relation to genotype and implication for tauopathies

Science.gov (United States)

Trabzuni, Daniah; Wray, Selina; Vandrovcova, Jana; Ramasamy, Adaikalavan; Walker, Robert; Smith, Colin; Luk, Connie; Gibbs, J. Raphael; Dillman, Allissa; Hernandez, Dena G.; Arepalli, Sampath; Singleton, Andrew B.; Cookson, Mark R.; Pittman, Alan M.; de Silva, Rohan; Weale, Michael E.; Hardy, John; Ryten, Mina

2012-01-01

The MAPT (microtubule-associated protein tau) locus is one of the most remarkable in neurogenetics due not only to its involvement in multiple neurodegenerative disorders, including progressive supranuclear palsy, corticobasal degeneration, Parksinson's disease and possibly Alzheimer's disease, but also due its genetic evolution and complex alternative splicing features which are, to some extent, linked and so all the more intriguing. Therefore, obtaining robust information regarding the expression, splicing and genetic regulation of this gene within the human brain is of immense importance. In this study, we used 2011 brain samples originating from 439 individuals to provide the most reliable and coherent information on the regional expression, splicing and regulation of MAPT available to date. We found significant regional variation in mRNA expression and splicing of MAPT within the human brain. Furthermore, at the gene level, the regional distribution of mRNA expression and total tau protein expression levels were largely in agreement, appearing to be highly correlated. Finally and most importantly, we show that while the reported H1/H2 association with gene level expression is likely to be due to a technical artefact, this polymorphism is associated with the expression of exon 3-containing isoforms in human brain. These findings would suggest that contrary to the prevailing view, genetic risk factors for neurodegenerative diseases at the MAPT locus are likely to operate by changing mRNA splicing in different brain regions, as opposed to the overall expression of the MAPT gene. PMID:22723018

Chronic intermittent hypoxia exerts CNS region-specific effects on rat microglial inflammatory and TLR4 gene expression.

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Stephanie M C Smith

Full Text Available Intermittent hypoxia (IH during sleep is a hallmark of sleep apnea, causing significant neuronal apoptosis, and cognitive and behavioral deficits in CNS regions underlying memory processing and executive functions. IH-induced neuroinflammation is thought to contribute to cognitive deficits after IH. In the present studies, we tested the hypothesis that IH would differentially induce inflammatory factor gene expression in microglia in a CNS region-dependent manner, and that the effects of IH would differ temporally. To test this hypothesis, adult rats were exposed to intermittent hypoxia (2 min intervals of 10.5% O2 for 8 hours/day during their respective sleep cycles for 1, 3 or 14 days. Cortex, medulla and spinal cord tissues were dissected, microglia were immunomagnetically isolated and mRNA levels of the inflammatory genes iNOS, COX-2, TNFα, IL-1β and IL-6 and the innate immune receptor TLR4 were compared to levels in normoxia. Inflammatory gene expression was also assessed in tissue homogenates (containing all CNS cells. We found that microglia from different CNS regions responded to IH differently. Cortical microglia had longer lasting inflammatory gene expression whereas spinal microglial gene expression was rapid and transient. We also observed that inflammatory gene expression in microglia frequently differed from that in tissue homogenates from the same region, indicating that cells other than microglia also contribute to IH-induced neuroinflammation. Lastly, microglial TLR4 mRNA levels were strongly upregulated by IH in a region- and time-dependent manner, and the increase in TLR4 expression appeared to coincide with timing of peak inflammatory gene expression, suggesting that TLR4 may play a role in IH-induced neuroinflammation. Together, these data indicate that microglial-specific neuroinflammation may play distinct roles in the effects of intermittent hypoxia in different CNS regions.

78 FR 25093 - Multistate Conservation Grant Program; Priority List and Approval for Conservation Projects

Science.gov (United States)

2013-04-29

... nongovernmental organizations that represent conservation organizations, sportsmen's and women's organizations... Regionally- coordinated Science and Collaboration. 9......... Compilation of Reservoir Habitat Arkansas Game...

Space, time and conservation laws

International Nuclear Information System (INIS)

Aronov, R.A.; Ugarov, V.A.

1978-01-01

The Neter theorem establishing correspondence between conservation laws and symmetry properties (space and time in particular) is considered. The theorem is based on one of the possible ways of finding equations of motion for a physical system. From a certain expression (action functional) equations of motion for a system can be obtained which do not contain new physical assertions in principal in comparison with the Newtonian laws. Neter suggested a way of deriving conservation laws by transforming space and time coordinates. Neter theorem consequences raise a number of problems: 1). Are conservation laws (energy, momentum) consequences of space and time symmetry properties. 2). Is it possible to obtain conservation laws in theory neglecting equations of motion. 3). What is of the primary importance: equations of motion, conservation laws or properties of space and time symmetry. It is shown that direct Neter theorem does not testify to stipulation of conservation laws by properties of space and time symmetry and symmetry properties of other non-space -time properties of material systems in objective reality. It says nothing of whether there is any subordination between symmetry properties and conservation laws

Conserved peptides within the E2 region of Hepatitis C virus induce humoral and cellular responses in goats

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El Shenawy Reem

2009-05-01

Full Text Available Abstract The reason(s why human antibodies raised against hepatitis C virus (HCV E2 epitopes do not offer protection against multiple viral infections may be related to either genetic variations among viral strains particularly within the hypervariable region-1 (HVR-1, low titers of anti E2 antibodies or interference of non neutralizing antibodies with the function of neutralizing antibodies. This study was designed to assess the immunogenic properties of genetically conserved peptides derived from the C-terminal region of HVR-1 as potential therapeutic and/or prophylactic vaccines against HCV infection. Goats immunized with E2-conserved synthetic peptides termed p36 (a.a 430–446, p37(a.a 517–531 and p38 (a.a 412–419 generated high titers of anti-p36, anti-p37 and anti-P38 antibody responses of which only anti- p37 and anti- p38 were neutralizing to HCV particles in sera from patients infected predominantly with genotype 4a. On the other hand anti-p36 exhibited weak viral neutralization capacity on the same samples. Animals super-immunized with single epitopes generated 2 to 4.5 fold higher titers than similar antibodies produced in chronic HCV patients. Also the studied peptides elicited approximately 3 fold increase in cell proliferation of specific antibody-secreting peripheral blood mononuclear cells (PBMC from immunized goats. These results indicate that, besides E1 derived peptide p35 (a.a 315–323 described previously by this laboratory, E2 conserved peptides p37 and p38 represent essential components of a candidate peptide vaccine against HCV infection.

Gene expression meta-analysis identifies chromosomal regions involved in ovarian cancer survival

DEFF Research Database (Denmark)

Thomassen, Mads; Jochumsen, Kirsten M; Mogensen, Ole

2009-01-01

the relation of gene expression and chromosomal position to identify chromosomal regions of importance for early recurrence of ovarian cancer. By use of *Gene Set Enrichment Analysis*, we have ranked chromosomal regions according to their association to survival. Over-representation analysis including 1...... using death (P = 0.015) and recurrence (P = 0.002) as outcome. The combined mutation score is strongly associated to upregulation of several growth factor pathways....

Regional differences in gene expression and promoter usage in aged human brains

KAUST Repository

Pardo, Luba M.; Rizzu, Patrizia; Francescatto, Margherita; Vitezic, Morana; Leday, Gwenaë l G.R.; Sanchez, Javier Simon; Khamis, Abdullah M.; Takahashi, Hazuki; van de Berg, Wilma D.J.; Medvedeva, Yulia A.; van de Wiel, Mark A.; Daub, Carsten O.; Carninci, Piero; Heutink, Peter

2013-01-01

To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites

A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.

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Joseph Grice

Full Text Available Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive.Here, we identify a shared sequence signature (syntax within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements from a set of conserved non-coding elements (CNEs. Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model.Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.

Water conservation in semiarid dryland agriculture

International Nuclear Information System (INIS)

Willis, W.O.

1980-01-01

Factors affecting water conservation in semiarid dryland regions are discussed. Because precipitation is the only source of water for plant growth in most semiarid regions, a good understanding of precipitation patterns (quantity, distribution, and their probable frequency) is needed for each dryland area. The various dryland practices, e.g. tillage, cultivars, residue management, fertility, erosion control, and grazing, must be considered as integral parts of an entire system to develop best management practices and to gain most efficient water conservation for food and fiber production. (author)

Conservation of transcription factor binding events predicts gene expression across species

OpenAIRE

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to funct...

Characterization of Cer-1 cis-regulatory region during early Xenopus development.

Science.gov (United States)

Silva, Ana Cristina; Filipe, Mário; Steinbeisser, Herbert; Belo, José António

2011-05-01

Cerberus-related molecules are well-known Wnt, Nodal, and BMP inhibitors that have been implicated in different processes including anterior–posterior patterning and left–right asymmetry. In both mouse and frog, two Cerberus-related genes have been isolated, mCer-1 and mCer-2, and Xcer and Xcoco, respectively. Until now, little is known about the mechanisms involved in their transcriptional regulation. Here, we report a heterologous analysis of the mouse Cerberus-1 gene upstream regulatory regions, responsible for its expression in the visceral endodermal cells. Our analysis showed that the consensus sequences for a TATA, CAAT, or GC boxes were absent but a TGTGG sequence was present at position -172 to -168 bp, relative to the ATG. Using a series of deletion constructs and transient expression in Xenopus embryos, we found that a fragment of 1.4 kb of Cer-1 promoter sequence could reproduce the endogenous expression pattern of Xenopus cerberus. A 0.7-kb mcer-1 upstream region was able to drive reporter expression to the involuting mesendodermal cells, while further deletions abolished reporter gene expression. Our results suggest that although no sequence similarity was found between mouse and Xenopus cerberus cis-regulatory regions, the signaling cascades regulating cerberus expression, during gastrulation, is conserved.

Mass, matter, materialization, mattergenesis and conservation of charge

International Nuclear Information System (INIS)

Tsan, Ung Chan

2013-01-01

Conservation of mass in classical physics and in chemistry is considered to be equivalent to conservation of matter and is a necessary condition together with other universal conservation laws to account for observed experiments. Indeed matter conservation is associated to conservation of building blocks (molecules, atoms, nucleons, quarks and leptons). Matter is massive but mass and matter are two distinct concepts even if conservation of mass and conservation of matter represent the same reality in classical physics and chemistry. Conservation of mass is a consequence of conservation of atoms. Conservation of mass is valid because in these cases it is a very good approximation, the variation of mass being tiny and undetectable by weighing. However, nuclear physics and particle physics clearly show that conservation of mass is not valid to express conservation of matter. Mass is one form of energy, is a positive quantity and plays a fundamental role in dynamics allowing particles to be accelerated. Origin of mass may be linked to recently discovered Higgs bosons. Matter conservation means conservation of baryonic number A and leptonic number L, A and L being algebraic numbers. Positive A and L are associated to matter particles, negative A and L are associated to antimatter particles. All known interactions do conserve matter thus could not generate, from pure energy, a number of matter particles different from that of number of antimatter particles. But our universe is material and neutral, this double message has to be deciphered simultaneously. Asymmetry of our universe demands an interaction which violates matter conservation but obeys all universal conservation laws, in particular conservation of electric charge Q. Expression of Q shows that conservation of (A–L) and total flavor TF are necessary and sufficient to conserve Q. Conservation of A and L is indeed a trivial case of conservation of (A–L) and is valid for all known interactions of the standard

Phoenix flagships: Conservation values and guanaco reintroduction in an anthropogenic landscape.

Science.gov (United States)

Lindon, Adrien; Root-Bernstein, Meredith

2015-09-01

Multiple forms of valuation contribute to public acceptance of conservation projects. Here, we consider how esthetic, intrinsic, and utilitarian values contribute to public attitudes toward a proposed reintroduction of guanaco (Lama guanicoe) in a silvopastoral system of central Chile. The nexus among landscape perceptions and valuations, support for reintroductions, and management of anthropogenic habitats is of increasing interest due to the proliferation of conservation approaches combining some or all of these elements, including rewilding and reconciliation ecology, for example. We assessed attitudes and values through an online questionnaire for residents of Santiago, Chile, using multiple methods including photo-montages and Likert scale assessments of value-based statements. We also combined the questionnaire approach with key informant interviews. We find strong support for the reintroduction of guanacos into the Chilean silvopastoral system ('espinal') in terms of esthetic and intrinsic values but less in terms of utilitarian values. Respondents preferred a scenario of espinal with guanacos and expressed interest in visiting it, as well as support for the reintroduction project on the basis that guanacos are native to central Chile. We suggest that reintroduced guanacos could serve as a 'phoenix flagship species' for espinal conservation, that is, a flagship species that has gone regionally extinct and is known but not associated with the region in the cultural memory. We consider how the lack of local cultural identity can both help and weaken phoenix flagships, which we expect to become more common.

On momentum conservation

International Nuclear Information System (INIS)

Karastoyanov, A.

1990-01-01

The relativistic law of momentum transformation shows that the sum of momenta of even isolated particles is not invariable in all inertial reference systems. This is connected with the relativistic change of kinetic energy and mass of a system of particles in result of internal interactions. The paper proposes a short and simple proof on the necessity of potential momentum. The momentum conservation law (for all interactions in the Minkowski world) is expressed in a generalized form. The constancy of the sum of kinetic and potential momentum of closed system of particles is shown. The energy conservation is a necessary condition. The potential momentum is defined as usual (e.g. as in the Berkeley Physics Course). (author). 13 refs

Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

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Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

2015-09-01

Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

Ranching and conservation in the Santa Cruz River Region, Sonora: Milpillas Case Study (Ganaderia y Conservacion en la Region del Rio Santa Cruz, Sonora: El Caso del Grupo Milpillas)

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Joaquin Murrieta-Saldivar

2006-01-01

The Sonoran Institute (SI) is a non-profit organization working with people toward common conservation goals. Two objectives guide the work of the Sonoran Institute in the Santa Cruz River Region in Sonora, Mexico: to establish projects with community participation that can result in tangible and long-lasting benefits to the environment, and to ensure success by...

Comparison of regional gene expression differences in the brains of the domestic dog and human

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Kennerly Erin

2004-11-01

Full Text Available Abstract Comparison of the expression profiles of 2,721 genes in the cerebellum, cortex and pituitary gland of three American Staffordshire terriers, one beagle and one fox hound revealed regional expression differences in the brain but failed to reveal marked differences among breeds, or even individual dogs. Approximately 85 per cent (42 of 49 orthologue comparisons of the regional differences in the dog are similar to those that differentiate the analogous human brain regions. A smaller percentage of human differences were replicated in the dog, particularly in the cortex, which may generally be evolving more rapidly than other brain regions in mammals. This study lays the foundation for detailed analysis of the population structure of transcriptional variation as it relates to cognitive and neurological phenotypes in the domestic dog.

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

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Abigail S Golden

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

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

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

1998-12-08

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

Regional specificity in deltamethrin induced cytochrome P450 expression in rat brain

International Nuclear Information System (INIS)

Yadav, Sanjay; Johri, Ashu; Dhawan, Alok; Seth, Prahlad K.; Parmar, Devendra

2006-01-01

Oral administration of deltamethrin (5 mg/kg x 7 or 15 or 21 days) was found to produce a time-dependent increase in the mRNA expression of xenobiotic metabolizing cytochrome P450 1A1 (CYP1A1), 1A2 and CYP2B1, 2B2 isoenzymes in rat brain. RT-PCR studies further showed that increase in the mRNA expression of these CYP isoenzymes observed after 21 days of exposure was region specific. Hippocampus exhibited maximum increase in the mRNA expression of CYP1A1, which was followed by pons-medulla, cerebellum and hypothalamus. The mRNA expression of CYP2B1 also exhibited maximum increase in the hypothalamus and hippocampus followed by almost similar increase in midbrain and cerebellum. In contrast, mRNA expression of CYP1A2 and CYP2B2, the constitutive isoenzymes exhibited relatively higher increase in pons-medulla, cerebellum and frontal cortex. Immunoblotting studies carried out with polyclonal antibody raised against rat liver CYP1A1/1A2 or CYP2B1/2B2 isoenzymes also showed increase in immunoreactivity comigrating with CYP1A1/1A2 or 2B1/2B2 in the microsomal fractions isolated from hippocampus, hypothalamus and cerebellum of rat treated with deltamethrin. Though the exact relationship of the xenobiotic metabolizing CYPs with the physiological function of the brain is yet to be clearly understood, the increase in the mRNA expression of the CYPs in the brain regions that regulate specific brain functions affected by deltamethrin have further indicated that modulation of these CYPs could be associated with the various endogenous functions of the brain

Molecular studies of Callithrix pygmaea (Primates, Platyrrhini based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

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Tagliaro Claudia Helena

2000-01-01

Full Text Available Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1 and a nuclear gene (intronic regions of the transferrin gene, suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.

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

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Leonardo Maltchik

2012-03-01

Full Text Available 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 (~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 differrent ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region.La selección de áreas prioritarias es un enorme desafío para la conservación de la biodiversidad. Métodos biogeográficos se han utilizado para identificar áreas prioritarias para la conservación, como la panbiogeografía. Este estudio tuvo como objetivo el empleo de herramientas panbiogeográficas, para identificar los patrones de distribución de los géneros de insectos acuáticos, en los sistemas de humedales de una extensa área de la región Neotropical (~280 000km², y así comparar la distribución de las

Current conserving theory at the operator level

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Yuan, Jiangtao; Wang, Yin; Wang, Jian

The basic assumption of quantum transport in mesoscopic systems is that the total charge inside the scattering region is zero. This means that the potential deep inside reservoirs is effectively screened and therefore the electric field at interface of scattering region is zero. Thus the current conservation condition can be satisfied automatically which is an important condition in mesoscopic transport. So far the current conserving ac theory is well developed by considering the displacement current which is due to Coulomb interaction if we just focus on the average current. However, the frequency dependent shot noise does not satisfy the conservation condition since we do not consider the current conservation at the operator level. In this work, we formulate a generalized current conserving theory at the operator level using non-equilibrium Green's function theory which could be applied to both average current and frequency dependent shot noise. A displacement operator is derived for the first time so that the frequency dependent correlation of displacement currents could be investigated. Moreover, the equilibrium shot noise is investigated and a generalized fluctuation-dissipation relationship is presented.

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

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Onuma, Manabu; Suzuki, Masatsugu; Ohtaishi, Noriyuki

2006-11-01

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.

Fine‐resolution conservation planning with limited climate‐change information

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Shah, Payal; Mallory, Mindy L.; Ando , Amy W.; Guntenspergen, Glenn R.

2017-01-01

Climate‐change induced uncertainties in future spatial patterns of conservation‐related outcomes make it difficult to implement standard conservation‐planning paradigms. A recent study translates Markowitz's risk‐diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate‐change scenarios for carrying out fine‐resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk‐return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate‐change information and full climate‐change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate‐change forecasts such that the best possible risk‐return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate‐change information could be reduced by 17% relative to other iterative approaches.

Evaluating private land conservation in the Cape Lowlands, South Africa.

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Von Hase, Amrei; Rouget, Mathieu; Cowling, Richard M

2010-10-01

Evaluation is important for judiciously allocating limited conservation resources and for improving conservation success through learning and strategy adjustment. We evaluated the application of systematic conservation planning goals and conservation gains from incentive-based stewardship interventions on private land in the Cape Lowlands and Cape Floristic Region, South Africa. We collected spatial and nonspatial data (2003-2007) to determine the number of hectares of vegetation protected through voluntary contractual and legally nonbinding (informal) agreements with landowners; resources spent on these interventions; contribution of the agreements to 5- and 20-year conservation goals for representation and persistence in the Cape Lowlands of species and ecosystems; and time and staff required to meet these goals. Conservation gains on private lands across the Cape Floristic Region were relatively high. In 5 years, 22,078 ha (27,800 ha of land) and 46,526 ha (90,000 ha of land) of native vegetation were protected through contracts and informal agreements, respectively. Informal agreements often were opportunity driven and cheaper and faster to execute than contracts. All contractual agreements in the Cape Lowlands were within areas of high conservation priority (identified through systematic conservation planning), which demonstrated the conservation plan's practical application and a high level of overlap between resource investment (approximately R1.14 million/year in the lowlands) and priority conservation areas. Nevertheless, conservation agreements met only 11% of 5-year and 9% of 20-year conservation goals for Cape Lowlands and have made only a moderate contribution to regional persistence of flora to date. Meeting the plan's conservation goals will take three to five times longer and many more staff members to maintain agreements than initially envisaged. © 2010 Society for Conservation Biology.

The regulation of CD5 expression in murine T cells

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Herzenberg Leonard A

2001-05-01

Full Text Available Abstract Background CD5 is a pan-T cell surface marker that is also present on a subset of B cells, B-1a cells.Functional and developmental subsets of T cells express characteristic CD5 levels that vary over roughly a 30-fold range. Previous investigators have cloned a 1.7 Kb fragment containing the CD5 promoter and showed that it can confer similar lymphocyte-specific expression pattern as observed for endogenous CD5 expression. Results We further characterize the CD5 promoter and identify minimal and regulatory regions on the CD5 promoter. Using a luciferase reporter system, we show that a 43 bp region on the CD5 promoter regulates CD5 expression in resting mouse thymoma EL4 T cells and that an Ets binding site within the 43 bp region mediates the CD5 expression. In addition, we show that Ets-1, a member of the Ets family of transcription factors, recognizes the Ets binding site in the electrophoretic mobility shift assay (EMSA. This Ets binding site is directly responsible for the increase in reporter activity when co-transfected with increasing amounts of Ets-1 expression plasmid. We also identify two additional evolutionarily-conserved regions in the CD5 promoter (CD5X and CD5Y and demonstrate the respective roles of the each region in the regulation of CD5 transcription. Conclusion Our studies define a minimal and regulatory promoter for CD5 and show that the CD5 expression level in T cells is at least partially dependent on the level of Ets-1 protein. Based on the findings in this report, we propose a model of CD5 transcriptional regulation in T cells.

Multiscale habitat suitability index models for priority landbirds in the Central Hardwoods and West Gulf Coastal Plain/Ouachitas Bird Conservation Regions

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John M. Tirpak; D. Todd Jones-Farrand; Frank R., III Thompson; Daniel J. Twedt; William B., III Uihlein

2009-01-01

Habitat Suitability Index (HSI) models were developed to assess habitat quality for 40 priority bird species in the Central Hardwoods and West Gulf Coastal Plain/Ouachitas Bird Conservation Regions. The models incorporated both site and landscape environmental variables from one of six nationally consistent datasets. Potential habitat was first defined from unique...

Connecting Asian Heritage Conservation to the Idea of Performative Regionalism: A Case of Community-Enhancing Design Interventions in the Historical Art District of Liulichang Beijing

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Diana Thamrin

2015-02-01

Full Text Available The active and sometimes ruthless modernisation in Asia has triggered an urgent need to secure the protection and continuation of its rich heritage and diverse regional attributes. However, as in the case of China, the Asian perspective of conservation is different from the West in terms of the nature or ways of design interventions produced and its purposes. This phenomenon has frequently triggered criticisms from heritage conservation professionals. Hence, the objective of this paper is to explore the interventions done on Asian heritage sites, taking the Liulichang Art District in Beijing as the case study, and analyze the positive influence they have brought. The paper starts by distinguishing the Asian concept and values of authenticity in conservation that differ from the West and how these principles have been applied in Liulichang, a famous ancient street known for the selling and practice of classical Chinese arts, mostly for Chinese painting. Using the phenomenological method of analysis, the paper further elaborates on the importance of community building in learning and appreciating the art of Chinese painting and discusses the positive impact made by the design interventions in Liulichang, particularly in terms of community engagement and creation of novel ways to accommodate traditional cultural practices of Chinese painting. Results reflect that the Asian perspective of conservation do not always follow the principle of minimum intervention favoured by the West, but how contemporary interventions could be merged into the heritage site to revive regional communities and cultural activities, connecting Asian architectural conservation with the design approach coined by Barbara Allen (2005 as Performative Regionalism, hence developing the idea and practice of this approach as a result of the discussion. Rather than merely following textual or scientific procedures like in the West, this approach requires a more experiential way of

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

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Recep Colak

2010-10-01

Full Text Available Computational prediction of functionally related groups of genes (functional modules from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented.We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB, by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples.We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

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Colak, Recep; Moser, Flavia; Chu, Jeffrey Shih-Chieh; Schönhuth, Alexander; Chen, Nansheng; Ester, Martin

2010-10-25

Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large

Advancing marine conservation in European and contiguous seas with the MarCons Action

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Stelios Katsanevakis

2017-01-01

Full Text Available Cumulative human impacts have led to the degradation of marine ecosystems and the decline of biodiversity in the European and contiguous seas. Effective conservation measures are urgently needed to reverse these trends. Conservation must entail societal choices, underpinned by human values and worldviews that differ between the countries bordering these seas. Social, economic and political heterogeneity adds to the challenge of balancing conservation with sustainable use of the seas. Comprehensive macro-regional coordination is needed to ensure effective conservation of marine ecosystems and biodiversity of this region. Under the European Union Horizon 2020 framework programme, the MarCons COST action aims to promote collaborative research to support marine management, conservation planning and policy development. This will be achieved by developing novel methods and tools to close knowledge gaps and advance marine conservation science. This action will provide support for the development of macro-regional and national policies through six key actions: to develop tools to analyse cumulative human impacts; to identify critical scientific and technical gaps in conservation efforts; to improve the resilience of the marine environment to global change and biological invasions; to develop frameworks for integrated conservation planning across terrestrial, freshwater, and marine environments; to coordinate marine conservation policy across national boundaries; and to identify effective governance approaches for marine protected area management. Achieving the objectives of these actions will facilitate the integration of marine conservation policy into macro-regional maritime spatial planning agendas for the European and contiguous seas, thereby offsetting the loss of biodiversity and ecosystem services in this region.

Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 protein.

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Petty, Tom J; Nishimura, Taisuke; Emamzadah, Soheila; Gabus, Caroline; Paszkowski, Jerzy; Halazonetis, Thanos D; Thore, Stéphane

2010-08-01

Of the known epigenetic control regulators found in plants, the Morpheus' molecule 1 (MOM1) protein is atypical in that the deletion of MOM1 does not affect the level of epigenetic marks controlling the transcriptional status of the genome. A short 197-amino-acid fragment of the MOM1 protein sequence can complement MOM1 deletion when coupled to a nuclear localization signal, suggesting that this region contains a functional domain that compensates for the loss of the full-length protein. Numerous constructs centred on the highly conserved MOM1 motif 2 (CMM2) present in these 197 residues have been generated and expressed in Escherichia coli. Following purification and crystallization screening, diamond-shaped single crystals were obtained that diffracted to approximately 3.2 A resolution. They belonged to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a=85.64, c=292.74 A. Structure determination is ongoing.

Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus’ molecule 1 protein

Science.gov (United States)

Petty, Tom J.; Nishimura, Taisuke; Emamzadah, Soheila; Gabus, Caroline; Paszkowski, Jerzy; Halazonetis, Thanos D.; Thore, Stéphane

2010-01-01

Of the known epigenetic control regulators found in plants, the Morpheus’ molecule 1 (MOM1) protein is atypical in that the deletion of MOM1 does not affect the level of epigenetic marks controlling the transcriptional status of the genome. A short 197-amino-acid fragment of the MOM1 protein sequence can complement MOM1 deletion when coupled to a nuclear localization signal, suggesting that this region contains a functional domain that compensates for the loss of the full-length protein. Numerous constructs centred on the highly conserved MOM1 motif 2 (CMM2) present in these 197 residues have been generated and expressed in Escherichia coli. Following purification and crystallization screening, diamond-shaped single crystals were obtained that diffracted to ∼3.2 Å resolution. They belonged to the trigonal space group P3121 (or P3221), with unit-cell parameters a = 85.64, c = 292.74 Å. Structure determination is ongoing. PMID:20693667

Nonlocal symmetries and nonlocal conservation laws of Maxwell's equations

International Nuclear Information System (INIS)

Anco, S.C.; Bluman, G.

1997-01-01

Nonlocal symmetries are obtained for Maxwell's equations in three space-time dimensions through the use of two potential systems involving scalar and vector potentials for the electromagnetic field. Corresponding nonlocal conservation laws are derived from these symmetries. The conservation laws yield nine functionally independent constants of motion which cannot be expressed in terms of the constants of motion arising from local conservation laws for space-time symmetries. These nine constants of motion represent additional conserved quantities for the electromagnetic field in three space endash time dimensions. copyright 1997 American Institute of Physics

Expression

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Wang-Xia Wang

2014-02-01

Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

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

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Kristopher J. L. Irizarry

2016-01-01

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

Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus.

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Alison P Lee

Full Text Available The vertebrate Lhx2 is a member of the LIM homeobox family of transcription factors. It is essential for the normal development of the forebrain, eye, olfactory system and liver as well for the differentiation of lymphoid cells. However, despite the highly restricted spatio-temporal expression pattern of Lhx2, nothing is known about its transcriptional regulation. In mammals and chicken, Crb2, Dennd1a and Lhx2 constitute a conserved linkage block, while the intervening Dennd1a is lost in the fugu Lhx2 locus. To identify functional enhancers of Lhx2, we predicted conserved noncoding elements (CNEs in the human, mouse and fugu Crb2-Lhx2 loci and assayed their function in transgenic mouse at E11.5. Four of the eight CNE constructs tested functioned as tissue-specific enhancers in specific regions of the central nervous system and the dorsal root ganglia (DRG, recapitulating partial and overlapping expression patterns of Lhx2 and Crb2 genes. There was considerable overlap in the expression domains of the CNEs, which suggests that the CNEs are either redundant enhancers or regulating different genes in the locus. Using a large set of CNEs (810 CNEs associated with transcription factor-encoding genes that express predominantly in the central nervous system, we predicted four over-represented 8-mer motifs that are likely to be associated with expression in the central nervous system. Mutation of one of them in a CNE that drove reporter expression in the neural tube and DRG abolished expression in both domains indicating that this motif is essential for expression in these domains. The failure of the four functional enhancers to recapitulate the complete expression pattern of Lhx2 at E11.5 indicates that there must be other Lhx2 enhancers that are either located outside the region investigated or divergent in mammals and fishes. Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers.

Extinction risks and the conservation of Madagascar's reptiles.

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Richard K B Jenkins

Full Text Available BACKGROUND: An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. METHODOLOGY/PRINCIPAL FINDINGS: Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. CONCLUSIONS/SIGNIFICANCE: With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in

Extinction risks and the conservation of Madagascar's reptiles.

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Jenkins, Richard K B; Tognelli, Marcelo F; Bowles, Philip; Cox, Neil; Brown, Jason L; Chan, Lauren; Andreone, Franco; Andriamazava, Alain; Andriantsimanarilafy, Raphali R; Anjeriniaina, Mirana; Bora, Parfait; Brady, Lee D; Hantalalaina, Elisoa F; Glaw, Frank; Griffiths, Richard A; Hilton-Taylor, Craig; Hoffmann, Michael; Katariya, Vineet; Rabibisoa, Nirhy H; Rafanomezantsoa, Jeannot; Rakotomalala, Domoina; Rakotondravony, Hery; Rakotondrazafy, Ny A; Ralambonirainy, Johans; Ramanamanjato, Jean-Baptiste; Randriamahazo, Herilala; Randrianantoandro, J Christian; Randrianasolo, Harison H; Randrianirina, Jasmin E; Randrianizahana, Hiarinirina; Raselimanana, Achille P; Rasolohery, Andriambolantsoa; Ratsoavina, Fanomezana M; Raxworthy, Christopher J; Robsomanitrandrasana, Eric; Rollande, Finoana; van Dijk, Peter P; Yoder, Anne D; Vences, Miguel

2014-01-01

An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of

Extinction Risks and the Conservation of Madagascar's Reptiles

Science.gov (United States)

Jenkins, Richard K. B.; Tognelli, Marcelo F.; Bowles, Philip; Cox, Neil; Brown, Jason L.; Chan, Lauren; Andreone, Franco; Andriamazava, Alain; Andriantsimanarilafy, Raphali R.; Anjeriniaina, Mirana; Bora, Parfait; Brady, Lee D.; Hantalalaina, Elisoa F.; Glaw, Frank; Griffiths, Richard A.; Hilton-Taylor, Craig; Hoffmann, Michael; Katariya, Vineet; Rabibisoa, Nirhy H.; Rafanomezantsoa, Jeannot; Rakotomalala, Domoina; Rakotondravony, Hery; Rakotondrazafy, Ny A.; Ralambonirainy, Johans; Ramanamanjato, Jean-Baptiste; Randriamahazo, Herilala; Randrianantoandro, J. Christian; Randrianasolo, Harison H.; Randrianirina, Jasmin E.; Randrianizahana, Hiarinirina; Raselimanana, Achille P.; Rasolohery, Andriambolantsoa; Ratsoavina, Fanomezana M.; Raxworthy, Christopher J.; Robsomanitrandrasana, Eric; Rollande, Finoana; van Dijk, Peter P.; Yoder, Anne D.; Vences, Miguel

2014-01-01

Background An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Methodology/Principal Findings Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. Conclusions/Significance With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and

Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs.

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Campoli, Chiara; Shtaya, Munqez; Davis, Seth J; von Korff, Maria

2012-06-21

The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1), HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in Triticeae species.

Efficient Conservation in a Utility-Maximization Framework

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Frank W. Davis

2006-06-01

Full Text Available Systematic planning for biodiversity conservation is being conducted at scales ranging from global to national to regional. The prevailing planning paradigm is to identify the minimum land allocations needed to reach specified conservation targets or maximize the amount of conservation accomplished under an area or budget constraint. We propose a more general formulation for setting conservation priorities that involves goal setting, assessing the current conservation system, developing a scenario of future biodiversity given the current conservation system, and allocating available conservation funds to alter that scenario so as to maximize future biodiversity. Under this new formulation for setting conservation priorities, the value of a site depends on resource quality, threats to resource quality, and costs. This planning approach is designed to support collaborative processes and negotiation among competing interest groups. We demonstrate these ideas with a case study of the Sierra Nevada bioregion of California.

Culture Development Planning in the Special Region of Yogyakarta (Management Planning of Cultural Heritage in Kotagede District based on Community Empowerment Conservation Model

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Eko Suryanti

2014-09-01

Full Text Available The Special Region of Yogyakarta is a cultural rich city with excellent cultural resources. Yogyakarta should manage their assets with long-term planning to keep the sustainability. There is a very unique planning process due to a combination of political, technocratic, participatory, top down and bottom up approaches. This planning process is comprehensive or integrated because its involved many actor from multisectoral, multidisciplinary, multi regulatory, and multi planning documents, etc. Local wisdoms have been coloring the planning documents. This study describe and analyze the cultural development planning in Yogyakarta especially on the Management Planning in Kotagede Cultural Heritage District. We used qualitative descriptive approach methods and Miles and Huberman analysis methods. Participation of community and Non Governmental Organization (NGO in conservation planning of cultural heritage in this area is very significant in simplify the government task because people have been more literate in planning, have database of cultural assets, and capable of making their own decisions for the future of the region. Participatory rural appraisal (PRA dan Rapid Rural Appraisal (RRA were integrated in the planning process of Kotagede Heritage District management, thus it becomes a model of cultural heritage with community empowerment-based conservation. Keywords: culture development planning, comprehensive planning, heritage cultural district, community empowerment-based conservation.

Role of Tibetan Buddhist monasteries in snow leopard conservation.

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Li, Juan; Wang, Dajun; Yin, Hang; Zhaxi, Duojie; Jiagong, Zhala; Schaller, George B; Mishra, Charudutt; McCarthy, Thomas M; Wang, Hao; Wu, Lan; Xiao, Lingyun; Basang, Lamao; Zhang, Yuguang; Zhou, Yunyun; Lu, Zhi

2014-02-01

The snow leopard (Panthera uncia) inhabits the rugged mountains in 12 countries of Central Asia, including the Tibetan Plateau. Due to poaching, decreased abundance of prey, and habitat degradation, it was listed as endangered by the International Union for Conservation of Nature in 1972. Current conservation strategies, including nature reserves and incentive programs, have limited capacities to protect snow leopards. We investigated the role of Tibetan Buddhist monasteries in snow leopard conservation in the Sanjiangyuan region in China's Qinghai Province on the Tibetan Plateau. From 2009 to 2011, we systematically surveyed snow leopards in the Sanjiangyuan region. We used the MaxEnt model to determine the relation of their presence to environmental variables (e.g., elevation, ruggedness) and to predict snow leopard distribution. Model results showed 89,602 km(2) of snow leopard habitat in the Sanjiangyuan region, of which 7674 km(2) lay within Sanjiangyuan Nature Reserve's core zones. We analyzed the spatial relation between snow leopard habitat and Buddhist monasteries and found that 46% of monasteries were located in snow leopard habitat and 90% were within 5 km of snow leopard habitat. The 336 monasteries in the Sanjiangyuan region could protect more snow leopard habitat (8342 km(2) ) through social norms and active patrols than the nature reserve's core zones. We conducted 144 household interviews to identify local herders' attitudes and behavior toward snow leopards and other wildlife. Most local herders claimed that they did not kill wildlife, and 42% said they did not kill wildlife because it was a sin in Buddhism. Our results indicate monasteries play an important role in snow leopard conservation. Monastery-based snow leopard conservation could be extended to other Tibetan Buddhist regions that in total would encompass about 80% of the global range of snow leopards. © 2013 Society for Conservation Biology.

Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective

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Hernando Curtidor

2017-12-01

Full Text Available Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparum conserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC-mHABP-T-cell receptor (TCR complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS, forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.

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

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Chiarello

2000-05-01

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 Ribeirão Preto, State of São 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.

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

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

2014-01-01

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

Gene family size conservation is a good indicator of evolutionary rates.

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Chen, Feng-Chi; Chen, Chiuan-Jung; Li, Wen-Hsiung; Chuang, Trees-Juen

2010-08-01

The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

The Mid-Atlantic Regional Wetland Conservation Effects Assessment Project

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Megan Lang; Greg McCarty; Mark Walbridge; Patrick Hunt; Tom Ducey; Clinton Church; Jarrod Miller; Laurel Kluber; Ali Sadeghi; Martin Rabenhorst; Amir Sharifi; In-Young Yeo; Andrew Baldwin; Margaret Palmer; Tom Fisher; Dan Fenstermaher; Sanchul Lee; Owen McDonough; Metthea Yepsen; Liza McFarland; Anne Gustafson; Rebecca Fox; Chris Palardy; William Effland; Mari-Vaughn Johnson; Judy Denver; Scott Ator; Joseph Mitchell; Dennis Whigham

2016-01-01

Wetlands impart many important ecosystem services, including maintenance of water quality, regulation of the climate and hydrological flows, and enhancement of biodiversity through the provision of food and habitat. The conversion of natural lands to agriculture has led to broad scale historic wetland loss, but current US Department of Agriculture conservation programs...

How Should Beta-Diversity Inform Biodiversity Conservation?

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Socolar, Jacob B; Gilroy, James J; Kunin, William E; Edwards, David P

2016-01-01

To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conservation properties of numerical integration methods for systems of ordinary differential equations

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Rosenbaum, J. S.

1976-01-01

If a system of ordinary differential equations represents a property conserving system that can be expressed linearly (e.g., conservation of mass), it is then desirable that the numerical integration method used conserve the same quantity. It is shown that both linear multistep methods and Runge-Kutta methods are 'conservative' and that Newton-type methods used to solve the implicit equations preserve the inherent conservation of the numerical method. It is further shown that a method used by several authors is not conservative.

Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

DEFF Research Database (Denmark)

Martens, Geert A; Jiang, Lei; Hellemans, Karine H

2011-01-01

The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those...... of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture...... microdissected beta cells, monitor adaptations of the beta cell phenotype to fasting, and retrieve possible conserved transcriptional regulators....

The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

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Baker, Katie; Bayer, Micha; Cook, Nicola; Dreißig, Steven; Dhillon, Taniya; Russell, Joanne; Hedley, Pete E; Morris, Jenny; Ramsay, Luke; Colas, Isabelle; Waugh, Robbie; Steffenson, Brian; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J

2014-01-01

The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes. PMID:24947331

Gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions.

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Sivrikoz, Emre; Timirci-Kahraman, Özlem; Ergen, Arzu; Zeybek, Ümit; Aksoy, Murat; Yanar, Fatih; İsbir, Turgay; Kurtoğlu, Mehmet

2015-01-01

The purpose of this study was to investigate the gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions and to correlate it with clinical features of plaque destabilization. The study included 44 endarterectomy specimens available from operated symptomatic carotid artery stenoses. The specimens were separated according to anatomic location: internal carotid artery (ICA), external carotid artery (ECA) and common carotid artery (CCA), and then stored in liquid nitrogen. The amounts of cDNA for elastin and fibulin-5 were determined by Quantitative real-time PCR (Q-RT-PCR). Target gene copy numbers were normalized using hypoxanthine-guanine phosphoribosyltransferase (HPRT1) gene. The delta-delta CT method was applied for relative quantification. Q-RT-PCR data showed that relative fibulin-5 gene expression was increased in ICA plaque regions when compared to CCA regions but not reaching significance (p=0.061). At the same time, no differences were observed in elastin mRNA level between different anatomic plaque regions (p>0.05). Moreover, elastin and fibulin-5 mRNA expression and clinical parameters were compared in ICA plaques versus CCA and ECA regions, respectively. Up-regulation of elastin and fibulin-5 mRNA levels in ICA were strongly correlated with family history of cardiovascular disease when compared to CCA (p<0.05). Up-regulation of fibulin-5 in ICA was significantly associated with diabetes, and elevated triglycerides and very low density lipoprotein (VLDL) when compared to ECA (p<0.05). The clinical significance is the differences between the proximal and distal regions of the lesion, associated with the ICA, CCA and ECA respectively, with increased fibulin-5 in the ICA region. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Seasonal use of conservation reserve program lands by white-tailed deer in east-central South Dakota

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Gould, Jeffrey H.; Jenkins, Kurt J.

1993-01-01

The Conservation Reserve Program (CRP_, a provision of the 1985 Food Security Act, subsidizes landowners to take highly erodible lands out of cultivation and seed them to perennial cover for 10years. In eastern South Dakota, 0.5 million ha were enrolled in the CRP from 1985 to 1990 (Agric. Stabilization and Conserv. Serv., Brookings, S.D., unpubl. Data), which represents the largest change in conservation land-use practices in the region since the 1956 Soil Bank Program (Goetz 1987).Although the CRP is anticipated to produce substantial benefits for some wildlife species, particularly ground-nesting birds, its significance to white-tailed deer (Odocoileus virginianus) in the northern Great Plains agricultural region is poorly understood. Higgins et al. (1987) speculated that proliferation of CRP grasslands may provide a missing habitat component in intensively managed farmland, thereby enhancing several species of wildlife, including white-tailed deer. Deer managers in the region have expressed concerns that improved cover associated with DRP plantings on private land could attract deer and reduce hunter success rates or lead to increased depredation of adjacent croplands or stored winter forages (L. Rice, S.D. Dep. Game, Fish, and Parks, Rapid City, pers. comm., 1989). Our objectives were to describe variation in deer use of CRP lands by season, diel period, and deer activity class as a means of assessing seasonal importance of CRP fields to white-tailed deer in agricultural Midwest.

Insular ecosystems of the southeastern United States—A regional synthesis to support biodiversity conservation in a changing climate

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Cartwright, Jennifer M.; Wolfe, William J.

2016-08-11

In the southeastern United States, insular ecosystems—such as rock outcrops, depression wetlands, high-elevation balds, flood-scoured riparian corridors, and insular prairies and barrens—occupy a small fraction of land area but constitute an important source of regional and global biodiversity, including concentrations of rare and endemic plant taxa. Maintenance of this biodiversity depends upon regimes of abiotic stress and disturbance, incorporating factors such as soil surface temperature, widely fluctuating hydrologic conditions, fires, flood scouring, and episodic droughts that may be subject to alteration by climate change. Over several decades, numerous localized, site-level investigations have yielded important information about the floristics, physical environments, and ecological dynamics of these insular ecosystems; however, the literature from these investigations has generally remained fragmented. This report consists of literature syntheses for eight categories of insular ecosystems of the southeastern United States, concerning (1) physical geography, (2) ecological determinants of community structures including vegetation dynamics and regimes of abiotic stress and disturbance, (3) contributions to regional and global biodiversity, (4) historical and current anthropogenic threats and conservation approaches, and (5) key knowledge gaps relevant to conservation, particularly in terms of climate-change effects on biodiversity. This regional synthesis was undertaken to discern patterns across ecosystems, identify knowledge gaps, and lay the groundwork for future analyses of climate-change vulnerability. Findings from this synthesis indicate that, despite their importance to regional and global biodiversity, insular ecosystems of the southeastern United States have been subjected to a variety of direct and indirect human alterations. In many cases, important questions remain concerning key determinants of ecosystem function. In particular, few

Tourism and the Conservation of Critically Endangered Frogs

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Morrison, Clare; Simpkins, Clay; Castley, J. Guy; Buckley, Ralf C.

2012-01-01

Protected areas are critical for the conservation of many threatened species. Despite this, many protected areas are acutely underfunded, which reduces their effectiveness significantly. Tourism is one mechanism to promote and fund conservation in protected areas, but there are few studies analyzing its tangible conservation outcomes for threatened species. This study uses the 415 IUCN critically endangered frog species to evaluate the contribution of protected area tourism revenue to conservation. Contributions were calculated for each species as the proportion of geographic range inside protected areas multiplied by the proportion of protected area revenues derived from tourism. Geographic ranges were determined from IUCN Extent of Occurrence maps. Almost 60% (239) of critically endangered frog species occur in protected areas. Higher proportions of total range are protected in Nearctic, Australasian and Afrotopical regions. Tourism contributions to protected area budgets ranged from 5–100%. These financial contributions are highest for developing countries in the Afrotropical, Indomalayan and Neotropical regions. Data for both geographic range and budget are available for 201 critically endangered frog species with proportional contributions from tourism to species protection ranging from 0.8–99%. Tourism's financial contributions to critically endangered frog species protection are highest in the Afrotropical region. This study uses a coarse measure but at the global scale it demonstrates that tourism has significant potential to contribute to global frog conservation efforts. PMID:22984440

From continental priorities to local conservation: a multi-level analysis for African tortoises.

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Pierluigi Bombi

Full Text Available Terrestrial tortoises are the most endangered group of vertebrates but they are still largely ignored for defining global conservation priorities. In this paper, we explored within a hierarchical framework the potential contribution of prioritization studies at the continental scale to the planning of local initiatives for the conservation of African tortoises at the regional level. First, we modeled the distribution of all the African tortoise species, we calculated three indicators of conservation priority (i.e., species richness, conservation value, and complementarity, and we carried out a gap analysis at continental scale. Second, we focused on the most important region for tortoise conservation and performed the same analyses at higher resolution. Finally, we compared the results from the two scales for understanding the degree to which they are complementary. Southern Africa emerged from the continental analysis as the most important region for tortoises. Within this area, the high-resolution analysis pointed out specific core sites for conservation. The relative degree of species protection was assessed similarly at the two different resolutions. Two species appeared particularly vulnerable at both scales. Priority indices calculated at high resolution were correlated to the values calculated for the corresponding cells at low resolution but the congruence was stronger for species richness. Our results suggest to integrate the calculation of conservation value and complementarity into a hierarchical framework driven by species richness. The advantages of large scale planning include its broad perspective on complementarity and the capability to identify regions with greatest conservation potential. In this light, continental analyses allow targeting fine scale studies toward regions with maximum priority. The regional analyses at fine scale allow planning conservation measure at a resolution similar to that required for the practical

Transient cerebral ischemia induces albumin expression in microglia only in the CA1 region of the gerbil hippocampus.

Science.gov (United States)

Park, Joon Ha; Park, Jin-A; Ahn, Ji Hyeon; Kim, Yang Hee; Kang, Il Jun; Won, Moo-Ho; Lee, Choong-Hyun

2017-07-01

Albumin, the most abundant plasma protein, is known to exhibit a neuroprotective effect in animal models of focal and global cerebral ischemia. In the present study, the expression and immunoreactivity of albumin was examined in the hippocampus following 5 min of transient cerebral ischemia in gerbils. Albumin immunoreactivity was observed in microglia of the CA1 hippocampal region 2 days post‑ischemic insult, and it was significantly increased at 4 days following ischemia-reperfusion. In addition, at 4 days post‑ischemic insult, albumin‑immunoreactive microglia were abundant in the stratum pyramidale of the CA1 region. The present results demonstrated that albumin was newly expressed post‑injury in microglia in the CA1 region, suggesting ischemia‑induced neuronal loss. Albumin expression may therefore be associated with ischemia‑induced delayed neuronal death in the CA1 region following transient cerebral ischemia.

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

Science.gov (United States)

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

2013-01-01

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

BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms.

Science.gov (United States)

Esteves, Francisco F; Springhorn, Alexander; Kague, Erika; Taylor, Erika; Pyrowolakis, George; Fisher, Shannon; Bier, Ethan

2014-09-01

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of "neural identity" gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages.

BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms.

Directory of Open Access Journals (Sweden)

Francisco F Esteves

2014-09-01

Full Text Available In a broad variety of bilaterian species the trunk central nervous system (CNS derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of "neural identity" gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs that control localized expression of the Drosophila msh and zebrafish (Danio rerio msxB in the dorsal central nervous system (CNS. Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages.

Some guiding concepts for conservation biology.

Science.gov (United States)

Lindenmayer, David; Hunter, Malcolm

2010-12-01

The search for generalities in ecology has often been thwarted by contingency and ecological complexity that limit the development of predictive rules. We present a set of concepts that we believe succinctly expresses some of the fundamental ideas in conservation biology. (1) Successful conservation management requires explicit goals and objectives. (2) The overall goal of biodiversity management will usually be to maintain or restore biodiversity, not to maximize species richness. (3) A holistic approach is needed to solve conservation problems. (4) Diverse approaches to management can provide diverse environmental conditions and mitigate risk. (5) Using nature's template is important for guiding conservation management, but it is not a panacea. (6) Focusing on causes not symptoms enhances efficacy and efficiency of conservation actions. (7) Every species and ecosystem is unique, to some degree. (8) Threshold responses are important but not ubiquitous. (9) Multiple stressors often exert critical effects on species and ecosystems. (10) Human values are variable and dynamic and significantly shape conservation efforts. We believe most conservation biologists will broadly agree these concepts are important. That said, an important part of the maturation of conservation biology as a discipline is constructive debate about additional or alternative concepts to those we have proposed here. Therefore, we have established a web-based, online process for further discussion of the concepts outlined in this paper and developing additional ones. © 2010 Society for Conservation Biology.

Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain.

Science.gov (United States)

Tan, Powell Patrick Cheng; French, Leon; Pavlidis, Paul

2013-01-01

An important goal in neuroscience is to understand gene expression patterns in the brain. The recent availability of comprehensive and detailed expression atlases for mouse and human creates opportunities to discover global patterns and perform cross-species comparisons. Recently we reported that the major source of variation in gene transcript expression in the adult normal mouse brain can be parsimoniously explained as reflecting regional variation in glia to neuron ratios, and is correlated with degree of connectivity and location in the brain along the anterior-posterior axis. Here we extend this investigation to two gene expression assays of adult normal human brains that consisted of over 300 brain region samples, and perform comparative analyses of brain-wide expression patterns to the mouse. We performed principal components analysis (PCA) on the regional gene expression of the adult human brain to identify the expression pattern that has the largest variance. As in the mouse, we observed that the first principal component is composed of two anti-correlated patterns enriched in oligodendrocyte and neuron markers respectively. However, we also observed interesting discordant patterns between the two species. For example, a few mouse neuron markers show expression patterns that are more correlated with the human oligodendrocyte-enriched pattern and vice-versa. In conclusion, our work provides insights into human brain function and evolution by probing global relationships between regional cell type marker expression patterns in the human and mouse brain.

Social-psychological principles of community-based conservation and conservancy motivation: attaining goals within an autonomy-supportive environment.

Science.gov (United States)

Decaro, Daniel; Stokes, Michael

2008-12-01

Community-based natural resource conservation programs in developing nations face many implementation challenges underpinned by social-psychological mechanisms. One challenge is garnering local support in an economically and socially sustainable fashion despite economic hardship and historical alienation from local resources. Unfortunately, conservationists' limited understanding of the social-psychological mechanisms underlying participatory conservation impedes the search for appropriate solutions. We address this issue by revealing key underlying social-psychological mechanisms of participatory conservation. Different administrative designs create social atmospheres that differentially affect endorsement of conservation goals. Certain forms of endorsement may be less effective motivators and less economically and socially sustainable than others. From a literature review we found that conservation initiatives endorsed primarily for nonautonomous instrumental reasons, such as to avoid economic fines or to secure economic rewards, are less motivating than those endorsed for autonomous reasons, such as for the opportunity for personal expression and growth. We suggest that successful participatory programs promote autonomous endorsement of conservation through an administrative framework of autonomy support-free and open democratic participation in management, substantive recognition and inclusion of local stakeholder identity, and respectful, noncoercive social interaction. This framework of the autonomy-supportive environment (self-determination theory) has important implications for future research into program design and incentive-based conservation and identifies a testable social-psychological theory of conservancy motivation.

Conservation and reclamation at Alberta's mineable oil sands

Energy Technology Data Exchange (ETDEWEB)

Purdy, B.; Richens, T. [Alberta Environment, Edmonton, AB (Canada)

2010-07-01

The regulatory foundation for oil sands in this region is established by the Energy Resources Conservation Board, Environmental Protection and Enhancement Act (EPEA), as well as the Water Act. This presentation discussed the regulatory foundation for conservation and reclamation in the mineable oil sands region. EPEA requirements and conservation objectives were identified. EPEA conservation and reclamation requirements stipulate that an operator must conserve and reclaim and obtain a reclamation certificate. EPEA approvals that were presented compared prescriptive standards versus meeting outcomes at certification. Operational and management challenges as well as the role of research networks and multi-stakeholder organizations were also addressed. Challenge facing the industry include progressive reclamation; tailings management and process-affected water; reclamation certification; integrated landscapes; soil handling and revegetation and monitoring and research. The presentation demonstrated that reclamation begins with mine planning and ends with certification. figs.

HIV-1 p24(gag derived conserved element DNA vaccine increases the breadth of immune response in mice.

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Viraj Kulkarni

Full Text Available Viral diversity is considered a major impediment to the development of an effective HIV-1 vaccine. Despite this diversity, certain protein segments are nearly invariant across the known HIV-1 Group M sequences. We developed immunogens based on the highly conserved elements from the p24(gag region according to two principles: the immunogen must (i include strictly conserved elements of the virus that cannot mutate readily, and (ii exclude both HIV regions capable of mutating without limiting virus viability, and also immunodominant epitopes located in variable regions. We engineered two HIV-1 p24(gag DNA immunogens that express 7 highly Conserved Elements (CE of 12-24 amino acids in length and differ by only 1 amino acid in each CE ('toggle site', together covering >99% of the HIV-1 Group M sequences. Altering intracellular trafficking of the immunogens changed protein localization, stability, and also the nature of elicited immune responses. Immunization of C57BL/6 mice with p55(gag DNA induced poor, CD4(+ mediated cellular responses, to only 2 of the 7 CE; in contrast, vaccination with p24CE DNA induced cross-clade reactive, robust T cell responses to 4 of the 7 CE. The responses were multifunctional and composed of both CD4(+ and CD8(+ T cells with mature cytotoxic phenotype. These findings provide a method to increase immune response to universally conserved Gag epitopes, using the p24CE immunogen. p24CE DNA vaccination induced humoral immune responses similar in magnitude to those induced by p55(gag, which recognize the virus encoded p24(gag protein. The inclusion of DNA immunogens composed of conserved elements is a promising vaccine strategy to induce broader immunity by CD4(+ and CD8(+ T cells to additional regions of Gag compared to vaccination with p55(gag DNA, achieving maximal cross-clade reactive cellular and humoral responses.

Analysis of gene expression profile microarray data in complex regional pain syndrome.

Science.gov (United States)

Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

2017-09-01

The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

Conservation of the primary structure, organization, and function of the human and mouse β-globin locus-activating regions

International Nuclear Information System (INIS)

Moon, A.M.; Ley, T.J.

1990-01-01

DNA sequences located in a region 6-18 kilobases (kb) upstream from the human ε-globin gene are known as the locus-activating region (LAR) or dominant control region. This region is thought to play a key role in chromatin organization of the β-like globin gene cluster during erythroid development. Since the human β-globin LAR is functional in mice, the authors reasoned that critical LAR sequence elements might be conserved between mice and humans. They therefore cloned murine genomic sequences homologous to one portion of the human LAR. They found that this murine DNA fragment (mouse LAR site II) and sequences homologous to human LAR sites I and III are located upstream from the mouse β-like globin gene cluster and determined that their locations relative to the cluster are similar to that of their human counterparts. The homologous site II sequences are 70% identical between mice and humans over a stretch of ∼800 base pairs. These results suggest that primary structural elements endash and the spatial organization of these elements endash are important for function of the β-globin LAR

Stated Preferences for Forest Conservation in Southern Finland

DEFF Research Database (Denmark)

Lehtonen, Emmi; Kuuluvainen, Jari; Pouta, Eija

% support decreasing forest conservation. An average willingness-to-pay for increased biodiversity conservation was 60-212 € per household per year, depending on the described project and measurement method. In addition to costs per household, the number of conserved biotopes and endangered plant and animal......This study analyses Finnish citizens’ valuations and attitudes towards a forest conservation programme for southern Finland and the Pohjanmaa region. In particular, Finnish households’ willingness to accept expenses through increased taxation to guarantee a certain level of biodiversity...... conservation was investigated. Contingent valuation (CV) and choice experiment (CE) methods were applied. According to the CV results, 74% of respondents are prepared to pay for increased conservation and 16% support increased conservation but are not willing to pay for it. A further 5% are indifferent and 5...

Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis.

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Xiumei Li

Full Text Available Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.

Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

International Nuclear Information System (INIS)

Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A.

2005-01-01

Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes

The identification and functional annotation of RNA structures conserved in vertebrates

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

2017-01-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-b......-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.......Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure......-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins...

Defining the demands and meeting the challenges of integrated bird conservation

Science.gov (United States)

Charles K. Baxter

2005-01-01

Understanding the demands of integration bird conservation begins with a critical assessment of the North American Bird Conservation Initiative's (NABCI) goal."Regionally-based, biologically-driven, landscape oriented partnerships delivering the full spectrum of bird conservation across the entirety of North America."

Small interfering RNA targeted to stem-loop II of the 5' untranslated region effectively inhibits expression of six HCV genotypes

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Dash Srikanta

2006-11-01

Full Text Available Abstract Background The antiviral action of interferon alpha targets the 5' untranslated region (UTR used by hepatitis C virus (HCV to translate protein by an internal ribosome entry site (IRES mechanism. Although this sequence is highly conserved among different clinical strains, approximately half of chronically infected hepatitis C patients do not respond to interferon therapy. Therefore, development of small interfering RNA (siRNA targeted to the 5'UTR to inhibit IRES mediated translation may represent an alternative approach that could circumvent the problem of interferon resistance. Results Four different plasmid constructs were prepared for intracellular delivery of siRNAs targeting the stem loop II-III of HCV 5' UTR. The effect of siRNA production on IRES mediated translation was investigated using chimeric clones between the gene for green fluorescence protein (GFP and IRES sequences of six different HCV genotypes. The siRNA targeted to stem loop II effectively mediated degradation of HCV IRES mRNA and inhibited GFP expression in the case of six different HCV genotypes, where as siRNAs targeted to stem loop III did not. Furthermore, intracytoplasmic expression of siRNA into transfected Huh-7 cells efficiently degraded HCV genomic RNA and inhibited core protein expression from infectious full-length infectious clones HCV 1a and HCV 1b strains. Conclusion These in vitro studies suggest that siRNA targeted to stem-loop II is highly effective inhibiting IRES mediated translation of the major genotypes of HCV. Stem-loop II siRNA may be a good target for developing an intracellular immunization strategy based antiviral therapy to inhibit hepatitis C virus strains that are not inhibited by interferon.

Importance of regional variation in conservation planning: A rangewide example of the Greater Sage-Grouse

Science.gov (United States)

Doherty, Kevin E.; Evans, Jeffrey S.; Coates, Peter S.; Juliusson, Lara; Fedy, Bradley C.

2016-01-01

We developed rangewide population and habitat models for Greater Sage-Grouse (Centrocercus urophasianus) that account for regional variation in habitat selection and relative densities of birds for use in conservation planning and risk assessments. We developed a probabilistic model of occupied breeding habitat by statistically linking habitat characteristics within 4 miles of an occupied lek using a nonlinear machine learning technique (Random Forests). Habitat characteristics used were quantified in GIS and represent standard abiotic and biotic variables related to sage-grouse biology. Statistical model fit was high (mean correctly classified = 82.0%, range = 75.4–88.0%) as were cross-validation statistics (mean = 80.9%, range = 75.1–85.8%). We also developed a spatially explicit model to quantify the relative density of breeding birds across each Greater Sage-Grouse management zone. The models demonstrate distinct clustering of relative abundance of sage-grouse populations across all management zones. On average, approximately half of the breeding population is predicted to be within 10% of the occupied range. We also found that 80% of sage-grouse populations were contained in 25–34% of the occupied range within each management zone. Our rangewide population and habitat models account for regional variation in habitat selection and the relative densities of birds, and thus, they can serve as a consistent and common currency to assess how sage-grouse habitat and populations overlap with conservation actions or threats over the entire sage-grouse range. We also quantified differences in functional habitat responses and disturbance thresholds across the Western Association of Fish and Wildlife Agencies (WAFWA) management zones using statistical relationships identified during habitat modeling. Even for a species as specialized as Greater Sage-Grouse, our results show that ecological context matters in both the strength of habitat selection (i

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

Science.gov (United States)

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

2011-12-01

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

Forest gene conservation from the perspective of the international community

Science.gov (United States)

M. Hosny El-Lakany

2017-01-01

conservation of forest genetic resources (FGR). After presenting internationally adopted definitions of some terms related to FGR, the characteristics of the current state of FGR conservation from a global perspective are summarized. Many international and regional organizations and institutions are engaged in the conservation of FGR at degrees ranging from...

Functional conservation of the Drosophila gooseberry gene and its evolutionary alleles.

Directory of Open Access Journals (Sweden)

Wei Liu

Full Text Available The Drosophila Pax gene gooseberry (gsb is required for development of the larval cuticle and CNS, survival to adulthood, and male fertility. These functions can be rescued in gsb mutants by two gsb evolutionary alleles, gsb-Prd and gsb-Pax3, which express the Drosophila Paired and mouse Pax3 proteins under the control of gooseberry cis-regulatory region. Therefore, both Paired and Pax3 proteins have conserved all the Gsb functions that are required for survival of embryos to fertile adults, despite the divergent primary sequences in their C-terminal halves. As gsb-Prd and gsb-Pax3 uncover a gsb function involved in male fertility, construction of evolutionary alleles may provide a powerful strategy to dissect hitherto unknown gene functions. Our results provide further evidence for the essential role of cis-regulatory regions in the functional diversification of duplicated genes during evolution.

Energy conservation programs of Pemex exploration and production, south region; Programas de ahorro de energia en Pemex exploracion y produccion, region sur

Energy Technology Data Exchange (ETDEWEB)

Gonzalez Milla, Guillermo; Garcia Juarez, Francisco; Alarcon Aleman, Jose Mauricio [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

1999-12-31

The technological developments of energy economizing equipment constitute a powerful tool for the conservation and saving of the electric energy in new or existing installations. Petroleos Mexicanos (PEMEX) Exploration and Production initiated in 1997 a program for energy economizing in the South region, for which the Instituto de Investigaciones Electricas, through its Unit for the Use of Energy, collaborated performing energy assessments in 115 buildings of the above mentioned region. This paper describes the employed methodology to carry on the energy assessment, which consisted in an analysis of each building and different options for energy economizing were presented, which was accompanied with cost-benefit studies. The results obtained show that the air conditioning equipment and lighting represent the most important loads permanently connected, therefore the study was concentrated in these two loads [Espanol] Los desarrollos tecnologicos de equipos ahorradores de energia constituyen una poderosa herramienta para la conservacion y el ahorro de energia electrica en instalaciones nuevas o existentes. Petroleos Mexicanos (PEMEX) Exploracion y Produccion inicio en 1997 un programa para el ahorro de energia en la region sur, para lo cual el Instituto de Investigaciones Electricas, a traves de la Unidad de Uso de Energia, colaboro realizando diagnosticos energeticos en 115 edificios de dicha region. En este documento se describe la metodologia utilizada para realizar el diagnostico energetico, el cual consistio en un analisis de cada edificio y se presentaron diversas opciones para ahorrar energia, lo cual se acompano de estudios de costo-beneficio. Los resultados obtenidos muestran que los equipos de aire acondicionado e iluminacion representan la parte mas importante de las cargas conectadas permanentemente, por lo que el estudio se concentro en estas dos cargas

Energy conservation programs of Pemex exploration and production, south region; Programas de ahorro de energia en Pemex exploracion y produccion, region sur

Energy Technology Data Exchange (ETDEWEB)

Gonzalez Milla, Guillermo; Garcia Juarez, Francisco; Alarcon Aleman, Jose Mauricio [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

1998-12-31

The technological developments of energy economizing equipment constitute a powerful tool for the conservation and saving of the electric energy in new or existing installations. Petroleos Mexicanos (PEMEX) Exploration and Production initiated in 1997 a program for energy economizing in the South region, for which the Instituto de Investigaciones Electricas, through its Unit for the Use of Energy, collaborated performing energy assessments in 115 buildings of the above mentioned region. This paper describes the employed methodology to carry on the energy assessment, which consisted in an analysis of each building and different options for energy economizing were presented, which was accompanied with cost-benefit studies. The results obtained show that the air conditioning equipment and lighting represent the most important loads permanently connected, therefore the study was concentrated in these two loads [Espanol] Los desarrollos tecnologicos de equipos ahorradores de energia constituyen una poderosa herramienta para la conservacion y el ahorro de energia electrica en instalaciones nuevas o existentes. Petroleos Mexicanos (PEMEX) Exploracion y Produccion inicio en 1997 un programa para el ahorro de energia en la region sur, para lo cual el Instituto de Investigaciones Electricas, a traves de la Unidad de Uso de Energia, colaboro realizando diagnosticos energeticos en 115 edificios de dicha region. En este documento se describe la metodologia utilizada para realizar el diagnostico energetico, el cual consistio en un analisis de cada edificio y se presentaron diversas opciones para ahorrar energia, lo cual se acompano de estudios de costo-beneficio. Los resultados obtenidos muestran que los equipos de aire acondicionado e iluminacion representan la parte mas importante de las cargas conectadas permanentemente, por lo que el estudio se concentro en estas dos cargas

Trading Water Conservation Credits: A Coordinative Approach for Enhanced Urban Water Reliability

Science.gov (United States)

Gonzales, P.; Ajami, N. K.

2016-12-01

Water utilities in arid and semi-arid regions are increasingly relying on water use efficiency and conservation to extend the availability of supplies. Despite spatial and institutional inter-dependency of many service providers, these demand-side management initiatives have traditionally been tackled by individual utilities operating in a silo. In this study, we introduce a new approach to water conservation that addresses regional synergies—a novel system of tradable water conservation credits. Under the proposed approach, utilities have the flexibility to invest in water conservation measures that are appropriate for their specific service area. When utilities have insufficient capacity for local cost-effective measures, they may opt to purchase credits, contributing to fund subsidies for utilities that do have that capacity and can provide the credits, while the region as whole benefits from more reliable water supplies. While similar programs have been used to address water quality concerns, to our knowledge this is one of the first studies proposing tradable credits for incentivizing water conservation. Through mathematical optimization, this study estimates the potential benefits of a trading program and demonstrates the institutional and economic characteristics needed for such a policy to be viable, including a proposed web platform to facilitate transparent regional planning, data-driven decision-making, and enhanced coordination of utilities. We explore the impacts of defining conservation targets tailored to local realities of utilities, setting credit prices, and different policy configurations. We apply these models to the case study of water utility members of the Bay Area Water Supply and Conservation Agency. Preliminary work shows that the diverse characteristics of these utilities present opportunities for the region to achieve conservation goals while maximizing the benefits to individual utilities through more flexible coordinative efforts.

Conservation biology in Asia: the major policy challenges.

Science.gov (United States)

McNeely, Jeffrey A; Kapoor-Vijay, Promila; Zhi, Lu; Olsvig-Whittaker, Linda; Sheikh, Kashif M; Smith, Andrew T

2009-08-01

With about half the world's human population and booming economies, Asia faces numerous challenges to its biodiversity. The Asia Section of the Society for Conservation Biology has identified some key policy issues in which significant progress can be made. These include developing new sources of funding for forest conservation; identifying potential impacts of energy alternatives on the conservation of biodiversity; curbing the trade in endangered species of plants and animals; a special focus on the conservation of mountain biodiversity; enhancing relevant research; ensuring that conservation biology contributes to major international conventions and funding mechanisms; using conservation biology to build a better understanding of zoonotic diseases; more effectively addressing human-animal conflicts; enhancing community-based conservation; and using conservation biology to help address the pervasive water-deficit problems in much of Asia. These challenges can be met through improved regional cooperation among the relevant stakeholders.

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Science.gov (United States)

Babbitt, Courtney C; Fedrigo, Olivier; Pfefferle, Adam D; Boyle, Alan P; Horvath, Julie E; Furey, Terrence S; Wray, Gregory A

2010-01-18

Despite striking differences in cognition and behavior between humans and our closest primate relatives, several studies have found little evidence for adaptive change in protein-coding regions of genes expressed primarily in the brain. Instead, changes in gene expression may underlie many cognitive and behavioral differences. Here, we used digital gene expression: tag profiling (here called Tag-Seq, also called DGE:tag profiling) to assess changes in global transcript abundance in the frontal cortex of the brains of 3 humans, 3 chimpanzees, and 3 rhesus macaques. A substantial fraction of transcripts we identified as differentially transcribed among species were not assayed in previous studies based on microarrays. Differentially expressed tags within coding regions are enriched for gene functions involved in synaptic transmission, transport, oxidative phosphorylation, and lipid metabolism. Importantly, because Tag-Seq technology provides strand-specific information about all polyadenlyated transcripts, we were able to assay expression in noncoding intragenic regions, including both sense and antisense noncoding transcripts (relative to nearby genes). We find that many noncoding transcripts are conserved in both location and expression level between species, suggesting a possible functional role. Lastly, we examined the overlap between differential gene expression and signatures of positive selection within putative promoter regions, a sign that these differences represent adaptations during human evolution. Comparative approaches may provide important insights into genes responsible for differences in cognitive functions between humans and nonhuman primates, as well as highlighting new candidate genes for studies investigating neurological disorders.

Disruption of a -35kb enhancer impairs CTCF binding and MLH1 expression in colorectal cells.

Science.gov (United States)

Liu, Qing; Thoms, Julie A; Nunez, Andrea C; Huang, Yizhou; Knezevic, Kathy; Packham, Deborah; Poulos, Rebecca C; Williams, Rachel; Beck, Dominik; Hawkins, Nicholas J; Ward, Robyn L; Wong, Jason W H; Hesson, Luke B; Sloane, Mathew A; Pimanda, John

2018-06-13

MLH1 is a major tumour suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified. Here we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1 expressing and non-expressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation and CRISPR-Cas9 mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter. A 1.8kb DNA fragment, 35kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9 mediated deletion of a core binding region impairs endogenous MLH1 expression. 5.4% of suspected Lynch syndrome patients have a rare single nucleotide variant (G>A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells. A CTCF bound region within the MLH1 -35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Copyright ©2018, American Association for Cancer Research.

Diversity, natural history and conservation of amphibians and reptiles from the San Vito Region, southwestern Costa Rica.

Science.gov (United States)

Santos-Barrera, Georgina; Pacheco, Jesus; Mendoza-Quijano, Fernando; Bolaños, Federico; Cháves, Gerardo; Daily, Gretchen C; Ehrlich, Paul R; Ceballos, Gerardo

2008-06-01

We present an inventory of the amphibians and reptiles of the San Vito de Coto Brus region, including the Las Cruces Biological Station, in southern Costa Rica, which is the result of a survey of the herpetofauna occurring in mountain forest fragments, pastures, coffee plantations, and other disturbed areas. We found 67 species, included 26 species of amphibians and of 41 of reptiles. We describe the distribution patterns of the community on the basis of the life zones, elevation, fragmentation, and degree of anthropogenic impact. We also provide some nouvelle data on the systematics of some select taxa, their geographical ranges, microhabitats, activity, and other relevant ecological and natural history features. Finally, we comment on the present conservation status of the herpetofauna in the region. Previous literature and collection records indicate a higher number of species occurring in this area, which suggests that some declines have occurred, especially of amphibians, in last decades.

Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region

Science.gov (United States)

Pinkney, Alfred E.; Driscoll, Charles T.; Evers, David C.; Hooper, Michael J.; Horan, Jeffrey; Jones, Jess W.; Lazarus, Rebecca S.; Marshall, Harold G.; Milliken, Andrew; Rattner, Barnett A.; Schmerfeld, John J.; Sparling, Donald W.

2015-01-01

The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public–private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena—freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures

Combining landscape-level conservation planning and biodiversity offset programs: a case study.

Science.gov (United States)

Underwood, Jared G

2011-01-01

Habitat loss is a major factor in the endangerment and extinction of species around the world. One promising strategy to balance continued habitat loss and biodiversity conservation is that of biodiversity offsets. However, a major concern with offset programs is their consistency with landscape-level conservation goals. While merging offset policies and landscape-level conservation planning is thought to provide advantages over a traditional disconnected approach, few such landscape-level conservation-offset plans have been designed and implemented, so the effectiveness of such a strategy remains uncertain. In this study, we quantitatively assess the conservation impact of combining landscape-level conservation planning and biodiversity offset programs by comparing regions of San Diego County, USA with the combined approach to regions with only an offset program. This comparison is generally very difficult due to a variety of complicating factors. We overcome these complications and quantify the benefits to rare and threatened species of implementing a combined approach by assessing the amount of each species' predicted distribution, and the number of documented locations, conserved in comparison to the same metric for areas with an offset policy alone. We found that adoption of the combined approach has increased conservation for many rare species, often 5-10 times more than in the comparison area, and that conservation has been focused in the areas most important for these species. The level of conservation achieved reduces uncertainty that these species will persist in the region into the future. This San Diego County example demonstrates the potential benefits of combining landscape-level conservation planning and biodiversity offset programs.

Preferential transcription of conserved rif genes in two phenotypically distinct Plasmodium falciparum parasite lines

DEFF Research Database (Denmark)

Wang, Christian W; Magistrado, Pamela A; Nielsen, Morten A

2009-01-01

transcribed in the VAR2CSA-expressing parasite line. In addition, two rif genes were found transcribed at early and late intra-erythrocyte stages independently of var gene transcription. Rif genes are organised in groups and inter-genomic conserved gene families, suggesting that RIFIN sub-groups may have......Plasmodium falciparum variant surface antigens (VSA) are targets of protective immunity to malaria. Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) and repetitive interspersed family (RIFIN) proteins are encoded by the two variable multigene families, var and rif genes, respectively...... novel rif gene groups, rifA1 and rifA2, containing inter-genomic conserved rif genes, were identified. All rifA1 genes were orientated head-to-head with a neighbouring Group A var gene whereas rifA2 was present in all parasite genomes as a single copy gene with a unique 5' untranslated region. Rif...

Hypothyroidism coordinately and transiently affects myelin protein gene expression in most rat brain regions during postnatal development.

Science.gov (United States)

Ibarrola, N; Rodríguez-Peña, A

1997-03-28

To assess the role of thyroid hormone on myelin gene expression, we have studied the effect of hypothyroidism on the mRNA steady state levels for the major myelin protein genes: myelin basic protein (MBP), proteolipid protein (PLP), myelin-associated glycoprotein (MAG) and 2':3'-cyclic nucleotide 3'-phosphodiesterase (CNP) in different rat brain regions, during the first postnatal month. We found that hypothyroidism reduces the levels of every myelin protein transcript, with striking differences between the different brain regions. Thus, in the more caudal regions, the effect of hypothyroidism was extremely modest, being only evident at the earlier stages of myelination. In contrast, in the striatum and the cerebral cortex the important decrease in the myelin protein transcripts is maintained beyond the first postnatal month. Therefore, thyroid hormone modulates in a synchronous fashion the expression of the myelin genes and the length of its effect depends on the brain region. On the other hand, hyperthyroidism leads to an increase of the major myelin protein transcripts above control values. Finally, lack of thyroid hormone does not change the expression of the oligodendrocyte progenitor-specific gene, the platelet derived growth factor receptor alpha.

Hsa-mir-182 suppresses lung tumorigenesis through down regulation of RGS17 expression in vitro

International Nuclear Information System (INIS)

Sun, Yihua; Fang, Rong; Li, Chenguang; Li, Li; Li, Fei; Ye, Xiaolei; Chen, Haiquan

2010-01-01

Lung cancer is one of the most devastating diseases worldwide. RGS17 is previously shown to be over-expressed in human lung adenocarcinomas and plays an important role in lung tumor growth. Here we have identified a miRNA, has-mir-182, involved in the regulation of RGS17 expression through two conserved sites located in its 3' UTR region. Consistently, endogenous RGS17 expression level is regulated by hsa-mir-182 in human lung cancer cell lines. Similar to the knockdown of RGS17, ectopic expression of hsa-mir-182 significantly inhibits lung cancer cell proliferation and anchorage-independent cell growth, which can be rescued by re-expression of RGS17. Taken together, these data have provided the first evidence of miRNA regulation of RGS17 expression in lung cancer.

Place-based and data-rich citizen science as a precursor for conservation action.

Science.gov (United States)

Haywood, Benjamin K; Parrish, Julia K; Dolliver, Jane

2016-06-01

Environmental education strategies have customarily placed substantial focus on enhancing ecological knowledge and literacy with the hope that, upon discovering relevant facts and concepts, participants will be better equipped to process and dissect environmental issues and, therefore, make more informed decisions. The assumption is that informed citizens will become active citizens--enthusiastically lobbying for, and participating in, conservation-oriented action. We surveyed and interviewed and used performance data from 432 participants in the Coastal Observation and Seabird Survey Team (COASST), a scientifically rigorous citizen science program, to explore measurable change in and links between understanding and action. We found that participation in rigorous citizen science was associated with significant increases in participant knowledge and skills; a greater connection to place and, secondarily, to community; and an increasing awareness of the relative impact of anthropogenic activities on local ecosystems specifically through increasing scientific understanding of the ecosystem and factors affecting it. Our results suggest that a place-based, data-rich experience linked explicitly to local, regional, and global issues can lead to measurable change in individual and collective action, expressed in our case study principally through participation in citizen science and community action and communication of program results to personal acquaintances and elected officials. We propose the following tenets of conservation literacy based on emergent themes and the connections between them explicit in our data: place-based learning creates personal meaning making; individual experience nested within collective (i.e., program-wide) experience facilitates an understanding of the ecosystem process and function at local and regional scales; and science-based meaning making creates informed concern (i.e., the ability to discern both natural and anthropogenic forcing

The role of trade-offs in biodiversity conservation planning: linking ...

Indian Academy of Sciences (India)

Unknown

[Faith D P and Walker P A 2002 The role of trade-offs in biodiversity conservation planning: linking local management, regional planning and global conservation efforts; J. Biosci. 27 (Suppl. 2) 393–407]. 1. Introduction. A reality of biodiversity conservation planning is that it requires taking into account many things other than ...

Recruitment of Language-, Emotion- and Speech-Timing Associated Brain Regions for Expressing Emotional Prosody: Investigation of Functional Neuroanatomy with fMRI.

Science.gov (United States)

Mitchell, Rachel L C; Jazdzyk, Agnieszka; Stets, Manuela; Kotz, Sonja A

2016-01-01

We aimed to progress understanding of prosodic emotion expression by establishing brain regions active when expressing specific emotions, those activated irrespective of the target emotion, and those whose activation intensity varied depending on individual performance. BOLD contrast data were acquired whilst participants spoke non-sense words in happy, angry or neutral tones, or performed jaw-movements. Emotion-specific analyses demonstrated that when expressing angry prosody, activated brain regions included the inferior frontal and superior temporal gyri, the insula, and the basal ganglia. When expressing happy prosody, the activated brain regions also included the superior temporal gyrus, insula, and basal ganglia, with additional activation in the anterior cingulate. Conjunction analysis confirmed that the superior temporal gyrus and basal ganglia were activated regardless of the specific emotion concerned. Nevertheless, disjunctive comparisons between the expression of angry and happy prosody established that anterior cingulate activity was significantly higher for angry prosody than for happy prosody production. Degree of inferior frontal gyrus activity correlated with the ability to express the target emotion through prosody. We conclude that expressing prosodic emotions (vs. neutral intonation) requires generic brain regions involved in comprehending numerous aspects of language, emotion-related processes such as experiencing emotions, and in the time-critical integration of speech information.

Recruitment of language-, emotion- and speech timing associated brain regions for expressing emotional prosody: Investigation of functional neuroanatomy with fMRI.

Directory of Open Access Journals (Sweden)

Rachel L. C. Mitchell

2016-10-01

Full Text Available We aimed to progress understanding of prosodic emotion expression by establishing brain regions active when expressing specific emotions, those activated irrespective of the target emotion, and those whose activation intensity varied depending on individual performance. BOLD contrast data were acquired whilst participants spoke nonsense words in happy, angry or neutral tones, or performed jaw-movements. Emotion-specific analyses demonstrated that when expressing angry prosody, activated brain regions included the inferior frontal and superior temporal gyri, the insula, and the basal ganglia. When expressing happy prosody, the activated brain regions also included the superior temporal gyrus, insula, and basal ganglia, with additional activation in the anterior cingulate. Conjunction analysis confirmed that the superior temporal gyrus and basal ganglia were activated regardless of the specific emotion concerned. Nevertheless, disjunctive comparisons between the expression of angry and happy prosody established that anterior cingulate activity was significantly higher for angry prosody than for happy prosody production. Degree of inferior frontal gyrus activity correlated with the ability to express the target emotion through prosody. We conclude that expressing prosodic emotions (vs neutral intonation requires generic brain regions involved in comprehending numerous aspects of language, emotion-related processes such as experiencing emotions, and in the time-critical integration of speech information.

Identification of Differentially Expressed Genes through Integrated Study of Alzheimer's Disease Affected Brain Regions.

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Nisha Puthiyedth

Full Text Available Alzheimer's disease (AD is the most common form of dementia in older adults that damages the brain and results in impaired memory, thinking and behaviour. The identification of differentially expressed genes and related pathways among affected brain regions can provide more information on the mechanisms of AD. In the past decade, several studies have reported many genes that are associated with AD. This wealth of information has become difficult to follow and interpret as most of the results are conflicting. In that case, it is worth doing an integrated study of multiple datasets that helps to increase the total number of samples and the statistical power in detecting biomarkers. In this study, we present an integrated analysis of five different brain region datasets and introduce new genes that warrant further investigation.The aim of our study is to apply a novel combinatorial optimisation based meta-analysis approach to identify differentially expressed genes that are associated to AD across brain regions. In this study, microarray gene expression data from 161 samples (74 non-demented controls, 87 AD from the Entorhinal Cortex (EC, Hippocampus (HIP, Middle temporal gyrus (MTG, Posterior cingulate cortex (PC, Superior frontal gyrus (SFG and visual cortex (VCX brain regions were integrated and analysed using our method. The results are then compared to two popular meta-analysis methods, RankProd and GeneMeta, and to what can be obtained by analysing the individual datasets.We find genes related with AD that are consistent with existing studies, and new candidate genes not previously related with AD. Our study confirms the up-regualtion of INFAR2 and PTMA along with the down regulation of GPHN, RAB2A, PSMD14 and FGF. Novel genes PSMB2, WNK1, RPL15, SEMA4C, RWDD2A and LARGE are found to be differentially expressed across all brain regions. Further investigation on these genes may provide new insights into the development of AD. In addition, we

The role of trade-offs in biodiversity conservation planning: linking ...

Indian Academy of Sciences (India)

Unknown

local management, regional planning and global conservation efforts .... conservation and the vertical axis indicates total amount of biodiversity protection “forgone” – not protected by .... tem services” that include such things as water quality,.

Impending conservation crisis for Southeast Asian amphibians.

Science.gov (United States)

Rowley, Jodi; Brown, Rafe; Bain, Raoul; Kusrini, Mirza; Inger, Robert; Stuart, Bryan; Wogan, Guin; Thy, Neang; Chan-Ard, Tanya; Trung, Cao Tien; Diesmos, Arvin; Iskandar, Djoko T; Lau, Michael; Ming, Leong Tzi; Makchai, Sunchai; Truong, Nguyen Quang; Phimmachak, Somphouthone

2010-06-23

With an understudied amphibian fauna, the highest deforestation rate on the planet and high harvesting pressures, Southeast Asian amphibians are facing a conservation crisis. Owing to the overriding threat of habitat loss, the most critical conservation action required is the identification and strict protection of habitat assessed as having high amphibian species diversity and/or representing distinctive regional amphibian faunas. Long-term population monitoring, enhanced survey efforts, collection of basic biological and ecological information, continued taxonomic research and evaluation of the impact of commercial trade for food, medicine and pets are also needed. Strong involvement of regional stakeholders, students and professionals is essential to accomplish these actions.

Cdna cloning and expression analyses of the isoflavone reductase-like gene of dendrobium officinale

International Nuclear Information System (INIS)

Qian, X.; Xu, S.Z.

2015-01-01

The full length of the isoflavone reductase-like gene (IRL) cDNA of Dendrobium officinale was cloned by using reverse transcription (RT) PCR combined with cDNA library, the IRL function was identified by Bioinformatics and prokaryotic expression analyses, and the IRL expression levels in the organs and tissues of D. officinale plants with different ages were determined by using real-time quantitative PCR (RT-qPCR). The results indicated that the full length of the cDNA of D. officinale IRL, DoIRL, was 1238 bp (accession no. KJ661023). Its open reading frame (ORF) was 930 bp which encoded 309 amino acids with a predicted molecular mass of 34 kDa, the 5 untranslated region (UTR) was 61 bp and the 3 UTR containing a poly (A) tail was 247 bp. The deduced amino acid sequence of DoIRL, DoIRL, was forecast to contain a NAD(P)H-binding motif (GGTGYIG) in the N-terminal region, two conserved N-glycosylation sites, a conserved nitrogen metabolite repression regulator (NmrA) domain and a phenylcoumaran benzylic ether reductase (PCBER) domain, to hold the nearest phylogenetic relationship with the PCBER of Striga asiatica, and to share both 73% identity with the isoflavone reductases-like (IRLs) of Cucumis sativus and Striga asiatica. In Escherichia coli 'BL21' cells, the DoIRL cDNA expression produced a protein band holding the predicted molecular mass of 34 kDa. DoIRL expressed in all organs and tissues of D. officinale plants with different ages at comparatively low levels, and the expression level in the leaves of the two-year-old plants was the highest. (author)

Infinite set of conservation laws for relativistic string

International Nuclear Information System (INIS)

Isaev, A.P.

1981-01-01

The solution of the Cauchy problem has been found. An infinite class of conserving values Jsub(α) for a free closed relativistic string has been constructed. Jsub(α) values characterize three-parametric generating functions of conservation laws. It is shown using particular examples that it is necessary to order subintegral expressions of quantum values Jsub(α) and do not disturb a property of commutativity with a hamiltonian to attach sense to these values [ru

Bird diversity, birdwatching tourism and conservation in Peru: a geographic analysis.

Directory of Open Access Journals (Sweden)

Liisa Puhakka

Full Text Available In the face of the continuing global biodiversity loss, it is important not only to assess the need for conservation, through e.g. gap analyses, but also to seek practical solutions for protecting biodiversity. Environmentally and socially sustainable tourism can be one such solution. We present a method to spatially link data on conservation needs and tourism-based economic opportunities, using bird-related tourism in Peru as an example. Our analysis highlighted areas in Peru where potential for such projects could be particularly high. Several areas within the central and northern Andean regions, as well as within the lowland Amazonian regions of Madre de Dios and Loreto emerge as promising for this type of activity. Mechanisms to implement conservation in these areas include e.g. conservation and ecotourism concessions, private conservation areas, and conservation easements. Some of these mechanisms also offer opportunities for local communities seeking to secure their traditional land ownership and use rights. (Spanish language abstract, Abstract S1.

Bird diversity, birdwatching tourism and conservation in Peru: a geographic analysis.

Science.gov (United States)

Puhakka, Liisa; Salo, Matti; Sääksjärvi, Ilari E

2011-01-01

In the face of the continuing global biodiversity loss, it is important not only to assess the need for conservation, through e.g. gap analyses, but also to seek practical solutions for protecting biodiversity. Environmentally and socially sustainable tourism can be one such solution. We present a method to spatially link data on conservation needs and tourism-based economic opportunities, using bird-related tourism in Peru as an example. Our analysis highlighted areas in Peru where potential for such projects could be particularly high. Several areas within the central and northern Andean regions, as well as within the lowland Amazonian regions of Madre de Dios and Loreto emerge as promising for this type of activity. Mechanisms to implement conservation in these areas include e.g. conservation and ecotourism concessions, private conservation areas, and conservation easements. Some of these mechanisms also offer opportunities for local communities seeking to secure their traditional land ownership and use rights. (Spanish language abstract, Abstract S1).

Biodiversity conservation in a changing climate: a review of threats and implications for conservation planning in Myanmar.

Science.gov (United States)

Rao, Madhu; Saw Htun; Platt, Steven G; Tizard, Robert; Poole, Colin; Than Myint; Watson, James E M

2013-11-01

High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development-the expectation is increased economic investments focused on the exploitation of the country's rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar's high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.

Bonneville Power Administration`s Commercial Sector Conservation Market.

Energy Technology Data Exchange (ETDEWEB)

Gordan, Frederick M. [Pacific Energy Associates, Inc. (United States)

1992-11-10

Bonneville has, as part of its resource plan, accepted targets for commercial conservation which are quite ambitious. To meet these targets, Bonneville will need to acquire as much cost-effective conservation as possible over the next twelve years. With this in mind, this document explores the relative importance of different commercial market segments and the types of assistance each market needs to install as many cost-effective conservation measures in as many buildings as possible. This document reviews Bonneville`s marketing environment and position, and suggests goals for commercial sector conservation marketing at Bonneville. Then it presents a broad market segmentation and series of additional demographic analyses. These analyses assess what groups of consumers Bonneville must reach to achieve most of the commercial conservation potential and what is needed to reach them. A final section reviews the success of Bonneville programs at reaching various markets. The market segmentation identifies different types of consumers and opportunities which would require distinct program approaches. Four large market segments are identified that have distinct program needs. Then four ``building life-cycle events`` are identified which provide important conservation opportunities and also require distinct program services. This creates a matrix of 16 cells which delineate distinct needs for program marketing. Each of the four key market segments manages at least 20% of the Region`s commercial floorspace.

Spatially explicit trends in the global conservation status of vertebrates.

Science.gov (United States)

Rodrigues, Ana S L; Brooks, Thomas M; Butchart, Stuart H M; Chanson, Janice; Cox, Neil; Hoffmann, Michael; Stuart, Simon N

2014-01-01

The world's governments have committed to preventing the extinction of threatened species and improving their conservation status by 2020. However, biodiversity is not evenly distributed across space, and neither are the drivers of its decline, and so different regions face very different challenges. Here, we quantify the contribution of regions and countries towards recent global trends in vertebrate conservation status (as measured by the Red List Index), to guide action towards the 2020 target. We found that>50% of the global deterioration in the conservation status of birds, mammals and amphibians is concentrated in nations (e.g. Cook Islands, Fiji, Mauritius, Seychelles, and Tonga), have achieved net improvements. Per capita wealth does not explain these patterns, with two of the richest countries - United States and Australia - fairing conspicuously poorly. Different countries were affected by different combinations of threats. Reducing global rates of biodiversity loss will require investment in the regions and countries with the highest responsibility for the world's biodiversity, focusing on conserving those species and areas most in peril and on reducing the drivers with the highest impacts.

SPAM1 (PH-20 protein and mRNA expression in the epididymides of humans and macaques: utilizing laser microdissection/RT-PCR

Directory of Open Access Journals (Sweden)

Zhang Hong

2003-08-01

Full Text Available Abstract Background The Sperm Adhesion Molecule 1 (SPAM1 is an important sperm surface hyaluronidase with at least three functions in mammalian fertilization. Previously our laboratory reported that in the mouse, in addition to its expression in the testis, Spam1 is synthesized in the epididymis where it is found in membranous vesicles in the principal cells of the epithelium in all three regions. Since SPAM1 is widely conserved among mammals the aim of the study was to determine if its expression pattern in the epididymis is conserved in rodents and primates. Methods We used laser microdissection (LM/RT-PCR on frozen and paraffin-embedded epididymal sections of humans (n = 3 and macaques (n = 2 as well as in situ transcript hybridization to determine if transcripts are present in the epididymal epithelium. Western analysis and immunohistochemistry were used to detect and confirm the protein expression, and hyaluronic acid substrate gel electrophoresis analyzed its hyaluronidase activity. An in silico analysis of the proximal promoter of SPAM1 was also performed to identify relevant putative transcription binding sites for the androgen receptor. Results We demonstrate that mRNA unique to SPAM1 is present in the principal cells of the epididymal epithelium in all individuals of both species studied. SPAM1 protein is present in all three regions of the epididymis, as well as the vas deferens, and is localized similarly to the transcripts. SPAM1 was shown to have hyaluronidase activity at pH 7.0. In the proximal promoter of SPAM1 were uncovered putative epididymal transcription factor binding sites including androgen receptor elements (AREs, consistent with epididymal expression. Conclusions These findings allow us to conclude that epididymal SPAM1 is conserved in at least two mammalian classes, rodents and primates. This conservation of expression suggests that the protein is likely to play an important function, possibly in sperm maturation.

Developmental regulation of gonadotropin-releasing hormone gene expression by the MSX and DLX homeodomain protein families.

Science.gov (United States)

Givens, Marjory L; Rave-Harel, Naama; Goonewardena, Vinodha D; Kurotani, Reiko; Berdy, Sara E; Swan, Christo H; Rubenstein, John L R; Robert, Benoit; Mellon, Pamela L

2005-05-13

Gonadotropin-releasing hormone (GnRH) is the central regulator of the hypothalamic-pituitary-gonadal axis, controlling sexual maturation and fertility in diverse species from fish to humans. GnRH gene expression is limited to a discrete population of neurons that migrate through the nasal region into the hypothalamus during embryonic development. The GnRH regulatory region contains four conserved homeodomain binding sites (ATTA) that are essential for basal promoter activity and cell-specific expression of the GnRH gene. MSX and DLX are members of the Antennapedia class of non-Hox homeodomain transcription factors that regulate gene expression and influence development of the craniofacial structures and anterior forebrain. Here, we report that expression patterns of the Msx and Dlx families of homeodomain transcription factors largely coincide with the migratory route of GnRH neurons and co-express with GnRH in neurons during embryonic development. In addition, MSX and DLX family members bind directly to the ATTA consensus sequences and regulate transcriptional activity of the GnRH promoter. Finally, mice lacking MSX1 or DLX1 and 2 show altered numbers of GnRH-expressing cells in regions where these factors likely function. These findings strongly support a role for MSX and DLX in contributing to spatiotemporal regulation of GnRH transcription during development.

Cloning, phylogeny, and regional expression of a Y5 receptor mRNA in the brain of the sea lamprey (Petromyzon marinus).

Science.gov (United States)

Pérez-Fernández, Juan; Megías, Manuel; Pombal, Manuel A

2014-04-01

The NPY receptors known as Y receptors are classified into three subfamilies, Y1, Y2, and Y5, and are involved in different physiological functions. The Y5 receptor is the only member of the Y5 subfamily, and it is present in all vertebrate groups, except for teleosts. Both molecular and pharmacological studies show that Y5 receptor is highly conserved during vertebrate evolution. Furthermore, this receptor is widely expressed in the mammalian brain, including the hypothalamus, where it is thought to take part in feeding and homeostasis regulation. Lampreys belong to the agnathan lineage, and they are thought to have branched out between the two whole-genome duplications that occurred in vertebrates. Therefore, they are in a key position for studies on the evolution of gene families in vertebrates. Here we report the cloning, phylogeny, and brain expression pattern of the sea lamprey Y5 receptor. In phylogenetic studies, the lamprey Y5 receptor clusters in a basal position, together with Y5 receptors of other vertebrates. The mRNA of this receptor is broadly expressed in the lamprey brain, being especially abundant in hypothalamic areas. Its expression pattern is roughly similar to that reported for other vertebrates and parallels the expression pattern of the Y1 receptor subtype previously described by our group, as it occurs in mammals. Altogether, these results confirm that a Y5 receptor is present in lampreys, thus being highly conserved during the evolution of vertebrates, and suggest that it is involved in many brain functions, the only known exception being teleosts. Copyright © 2013 Wiley Periodicals, Inc.

Arid Green Infrastructure for Water Control and Conservation ...

Science.gov (United States)

Green infrastructure is an approach to managing wet weather flows using systems and practices that mimic natural processes. It is designed to manage stormwater as close to its source as possible and protect the quality of receiving waters. Although most green infrastructure practices were first developed in temperate climates, green infrastructure also can be a cost-effective approach to stormwater management and water conservation in arid and semi-arid regions, such as those found in the western and southwestern United States. Green infrastructure practices can be applied at the site, neighborhood and watershed scales. In addition to water management and conservation, implementing green infrastructure confers many social and economic benefits and can address issues of environmental justice. The U.S. Environmental Protection Agency (EPA) commissioned a literature review to identify the state-of-the science practices dealing with water control and conservation in arid and semi-arid regions, with emphasis on these regions in the United States. The search focused on stormwater control measures or practices that slow, capture, treat, infiltrate and/or store runoff at its source (i.e., green infrastructure). The material in Chapters 1 through 3 provides background to EPA’s current activities related to the application of green infrastructure practices in arid and semi-arid regions. An introduction to the topic of green infrastructure in arid and semi-arid regions i

Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.

Science.gov (United States)

Sato, Mitsuhiko P; Makino, Takashi; Kawata, Masakado

2016-02-09

Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning

Different expression patterns of genes from the exo-xis region of bacteriophage λ and Shiga toxin-converting bacteriophage Ф24B following infection or prophage induction in Escherichia coli.

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Sylwia Bloch

Full Text Available Lambdoid bacteriophages serve as useful models in microbiological and molecular studies on basic biological process. Moreover, this family of viruses plays an important role in pathogenesis of enterohemorrhagic Escherichia coli (EHEC strains, as they are carriers of genes coding for Shiga toxins. Efficient expression of these genes requires lambdoid prophage induction and multiplication of the phage genome. Therefore, understanding the mechanisms regulating these processes appears essential for both basic knowledge and potential anti-EHEC applications. The exo-xis region, present in genomes of lambdoid bacteriophages, contains highly conserved genes of largely unknown functions. Recent report indicated that the Ea8.5 protein, encoded in this region, contains a newly discovered fused homeodomain/zinc-finger fold, suggesting its plausible regulatory role. Moreover, subsequent studies demonstrated that overexpression of the exo-xis region from a multicopy plasmid resulted in impaired lysogenization of E. coli and more effective induction of λ and Ф24B prophages. In this report, we demonstrate that after prophage induction, the increase in phage DNA content in the host cells is more efficient in E. coli bearing additional copies of the exo-xis region, while survival rate of such bacteria is lower, which corroborated previous observations. Importantly, by using quantitative real-time reverse transcription PCR, we have determined patterns of expressions of particular genes from this region. Unexpectedly, in both phages λ and Ф24B, these patterns were significantly different not only between conditions of the host cells infection by bacteriophages and prophage induction, but also between induction of prophages with various agents (mitomycin C and hydrogen peroxide. This may shed a new light on our understanding of regulation of lambdoid phage development, depending on the mode of lytic cycle initiation.

Analysis of a conserved RGE/RGD motif in HCV E2 in mediating entry

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Rong Lijun

2009-01-01

Full Text Available Abstract Background Hepatitis C virus (HCV encodes two transmembrane glycoproteins E1 and E2 which form a heterodimer. E1 is believed to mediate fusion while E2 has been shown to bind cellular receptors. It is clear that HCV uses a multi-receptor complex to gain entry into susceptible cells, however key elements of this complex remain elusive. In this study, the role of a highly conserved RGE/RGD motif of HCV E2 glycoprotein in viral entry was examined. The effect of each substitution mutation in this motif was tested by challenging susceptible cell lines with mutant HCV E1E2 pseudotyped viruses generated using a lentiviral system (HCVpp. In addition to assaying infectivity, producer cell expression and HCVpp incorporation of HCV E2 proteins, CD81 binding profiles, and conformation of mutants were examined. Results Based on these characteristics, mutants either displayed wt characteristics (high infectivity [≥ 90% of wt HCVpp], CD81 binding, E1E2 expression, and incorporation into viral particles and proper conformation or very low infectivity (≤ 20% of wt HCVpp. Only amino acid substitutions of the 3rd position (D or E resulted in wt characteristics as long as the negative charge was maintained or a neutral alanine was introduced. A change in charge to a positive lysine, disrupted HCVpp infectivity at this position. Conclusion Although most amino acid substitutions within this conserved motif displayed greatly reduced HCVpp infectivity, they retained soluble CD81 binding, proper E2 conformation, and incorporation into HCVpp. Our results suggest that although RGE/D is a well-defined integrin binding motif, in this case the role of these three hyperconserved amino acids does not appear to be integrin binding. As the extent of conservation of this region extends well beyond these three amino acids, we speculate that this region may play an important role in the structure of HCV E2 or in mediating the interaction with other factor(s during

Brain region-specific altered expression and association of mitochondria-related genes in autism.

Science.gov (United States)

Anitha, Ayyappan; Nakamura, Kazuhiko; Thanseem, Ismail; Yamada, Kazuo; Iwayama, Yoshimi; Toyota, Tomoko; Matsuzaki, Hideo; Miyachi, Taishi; Yamada, Satoru; Tsujii, Masatsugu; Tsuchiya, Kenji J; Matsumoto, Kaori; Iwata, Yasuhide; Suzuki, Katsuaki; Ichikawa, Hironobu; Sugiyama, Toshiro; Yoshikawa, Takeo; Mori, Norio

2012-11-01

Mitochondrial dysfunction (MtD) has been observed in approximately five percent of children with autism spectrum disorders (ASD). MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA). Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG), motor cortex (MC) and thalamus (THL)) from autism patients (n=8) and controls (n=10) were obtained from the Autism Tissue Program (Princeton, NJ, USA). Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct) method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2), neurofilament, light polypeptide (NEFL) and solute carrier family 25, member 27 (SLC25A27) showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066) and SLC25A27 (P = 0.046; Z-score 1.990) showed genetic association with autism in Caucasian and Japanese samples, respectively. The expression of DNAJC19, DNM1L, LRPPRC

Brain region-specific altered expression and association of mitochondria-related genes in autism

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Anitha Ayyappan

2012-11-01

Full Text Available Abstract Background Mitochondrial dysfunction (MtD has been observed in approximately five percent of children with autism spectrum disorders (ASD. MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA. Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. Methods For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG, motor cortex (MC and thalamus (THL from autism patients (n=8 and controls (n=10 were obtained from the Autism Tissue Program (Princeton, NJ, USA. Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Results Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2, neurofilament, light polypeptide (NEFL and solute carrier family 25, member 27 (SLC25A27 showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066 and SLC25A27 (P = 0.046; Z-score 1.990 showed genetic association with autism in Caucasian and Japanese samples, respectively. The

Structure and expression of the Xenopus retinoblastoma gene.

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Destrée, O H; Lam, K T; Peterson-Maduro, L J; Eizema, K; Diller, L; Gryka, M A; Frebourg, T; Shibuya, E; Friend, S H

1992-09-01

We have cloned a Xenopus homology (XRb1) of the human retinoblastoma susceptibility gene. DNA sequence analysis shows that the XRb1 gene product is highly conserved in many regions. The leucine repeat motif and many of the potential cdc2 phosphorylation sites, as well as potential sites for other kinases, are retained. The region of the protein homologous to the SV40 T antigen binding site and the basic region directly C-terminal to the E1A binding site are all conserved. XRb1 gene expression at the RNA level was studied by Northern blot analysis. Transcripts of 4.2 and 10-kb are present as maternal RNA stores in the oocyte. While the 4.2-kb product is stable until at least the mid-blastula stage, the 10-kb transcript is selectively degraded. Between stages 11 and 13 the 10-kb transcript reappears and also a minor product of approximately 11 kb becomes apparent. Both the 4.2- and the 10-kb transcripts remain present until later stages of development and are also present in all adult tissues examined, although at differing levels. Antibodies raised against human p105Rb which recognize the protein product of the XRb1 gene, pXRb1, detect the Xenopus 99-kDa protein prior to the mid-blastula stage, but at lower levels than at later stages in development.

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

Science.gov (United States)

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

2009-02-01

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

National Proceedings: Forest and Conservation Nursery Associations-2007

Science.gov (United States)

Kas Dumroese; L. E. Riley

2008-01-01

These proceedings are a compilation of the papers that were presented at the regional meetings of the forest and conservation nursery associations in the United States and Canada in 2007. The Northeastern Forest and Conservation Nursery Association meeting was held July 16 to 19 at the Grappone Conference Center in Concord, NH. The meeting was hosted by the New...

Prioritizing land and sea conservation investments to protect coral reefs.

Science.gov (United States)

Klein, Carissa J; Ban, Natalie C; Halpern, Benjamin S; Beger, Maria; Game, Edward T; Grantham, Hedley S; Green, Alison; Klein, Travis J; Kininmonth, Stuart; Treml, Eric; Wilson, Kerrie; Possingham, Hugh P

2010-08-30

Coral reefs have exceptional biodiversity, support the livelihoods of millions of people, and are threatened by multiple human activities on land (e.g. farming) and in the sea (e.g. overfishing). Most conservation efforts occur at local scales and, when effective, can increase the resilience of coral reefs to global threats such as climate change (e.g. warming water and ocean acidification). Limited resources for conservation require that we efficiently prioritize where and how to best sustain coral reef ecosystems. Here we develop the first prioritization approach that can guide regional-scale conservation investments in land- and sea-based conservation actions that cost-effectively mitigate threats to coral reefs, and apply it to the Coral Triangle, an area of significant global attention and funding. Using information on threats to marine ecosystems, effectiveness of management actions at abating threats, and the management and opportunity costs of actions, we calculate the rate of return on investment in two conservation actions in sixteen ecoregions. We discover that marine conservation almost always trumps terrestrial conservation within any ecoregion, but terrestrial conservation in one ecoregion can be a better investment than marine conservation in another. We show how these results could be used to allocate a limited budget for conservation and compare them to priorities based on individual criteria. Previous prioritization approaches do not consider both land and sea-based threats or the socioeconomic costs of conserving coral reefs. A simple and transparent approach like ours is essential to support effective coral reef conservation decisions in a large and diverse region like the Coral Triangle, but can be applied at any scale and to other marine ecosystems.

Novel urban ecosystems, biodiversity, and conservation

International Nuclear Information System (INIS)

Kowarik, Ingo

2011-01-01

With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. - Highlights: → This paper reviews biotic responses to urbanization and urban conservation approaches. → Cities may be rich in both native and nonnative species. → Urban habitats cannot replace the functionality of natural remnants. → However, even novel urban habitats may harbour rare and endangered species. → Conservation approaches should consider the perspective of novel urban ecosystems. - This paper reviews the ways in which biodiversity is affected by urbanization and argues for expanding urban conservation approaches.

Novel urban ecosystems, biodiversity, and conservation

Energy Technology Data Exchange (ETDEWEB)

Kowarik, Ingo, E-mail: kowarik@tu-berlin.de [Department of Ecology, Technische Universitaet Berlin, Rothenburgstr. 12, D 12165 Berlin (Germany)

2011-08-15

With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. - Highlights: > This paper reviews biotic responses to urbanization and urban conservation approaches. > Cities may be rich in both native and nonnative species. > Urban habitats cannot replace the functionality of natural remnants. > However, even novel urban habitats may harbour rare and endangered species. > Conservation approaches should consider the perspective of novel urban ecosystems. - This paper reviews the ways in which biodiversity is affected by urbanization and argues for expanding urban conservation approaches.

Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

DEFF Research Database (Denmark)

Martens, Geert A; Jiang, Lei; Hellemans, Karine H

2011-01-01

The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those...... of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture...

Identification of conserved regions and residues within Hedgehog acyltransferase critical for palmitoylation of Sonic Hedgehog.

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John A Buglino

2010-06-01

Full Text Available 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.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 K(m and V(max for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants.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.

Brain regional differences in social encounter-induced Fos expression in male and female rats after post-weaning social isolation.

Science.gov (United States)

Ahern, Megan; Goodell, Dayton J; Adams, Jessica; Bland, Sondra T

2016-01-01

Early life adversity has been related to a number of psychological disorders including mood and other disorders that can manifest as inappropriate or aggressive responses to social challenges. The present study used post-weaning social isolation (PSI) in rats, a model of early life adversity, to examine its effects on Fos protein expression produced by exposure to a novel social encounter. We have previously reported that the social encounter-induced increase in Fos expression in the medial prefrontal cortex observed in group-housed controls (GRP) was attenuated in rats that had experienced PSI. Here we assessed Fos expression in other brain regions thought to be involved in emotion regulation and social behavior. Male and female rats were housed in same-sex groups or in isolation (ISO) for 4 weeks beginning on postnatal day (P) 21 and were exposed to a single 15 min social encounter with a novel same-sex conspecific on P49. Fos positive cells were assessed using immunohistochemistry in 16 regions within the forebrain. Exposure to a novel conspecific increased Fos expression in the forebrain of GRP rats in a region- and sex-specific fashion. This increase was blunted or absent in ISO rats within many regions including cortical regions, thalamus, habenula, dentate gyrus, lateral septum, and basolateral amygdala. In several regions, the increase in Fos was greater in male than in female group housed rats. Negative relationships were observed between social interactions and Fos in some regions. Forebrain hypofunction produced by early-life adversity may be involved in socially inappropriate behavior. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparative gene expression between two yeast species

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Guan Yuanfang

2013-01-01

Full Text Available Abstract Background Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such comparisons is often limited by biased sampling of expression conditions and incomplete knowledge of gene functions across species. To address these challenges, we previously systematically generated expression profiles in Saccharomyces bayanus to maximize functional coverage as compared to an existing Saccharomyces cerevisiae data repository. Results In this paper, we take advantage of these two data repositories to compare patterns of ortholog expression in a wide variety of conditions. First, we developed a scalable metric for expression divergence that enabled us to detect a significant correlation between sequence and expression conservation on the global level, which previous smaller-scale expression studies failed to detect. Despite this global conservation trend, between-species gene expression neighborhoods were less well-conserved than within-species comparisons across different environmental perturbations, and approximately 4% of orthologs exhibited a significant change in co-expression partners. Furthermore, our analysis of matched perturbations collected in both species (such as diauxic shift and cell cycle synchrony demonstrated that approximately a quarter of orthologs exhibit condition-specific expression pattern differences. Conclusions Taken together, these analyses provide a global view of gene expression patterns between two species, both in terms of the conditions and timing of a gene's expression as well as co-expression partners. Our results provide testable hypotheses that will direct future experiments to determine how these changes may be specified in the genome.

Integrated conservation planning for coral reefs: Designing conservation zones for multiple conservation objectives in spatial prioritisation

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Rafael A. Magris

2017-07-01

Full Text Available Decision-makers focus on representing biodiversity pattern, maintaining connectivity, and strengthening resilience to global warming when designing marine protected area (MPA systems, especially in coral reef ecosystems. The achievement of these broad conservation objectives will likely require large areas, and stretch limited funds for MPA implementation. We undertook a spatial prioritisation of Brazilian coral reefs that considered two types of conservation zones (i.e. no-take and multiple use areas and integrated multiple conservation objectives into MPA planning, while assessing the potential impact of different sets of objectives on implementation costs. We devised objectives for biodiversity, connectivity, and resilience to global warming, determined the extent to which existing MPAs achieved them, and designed complementary zoning to achieve all objectives combined in expanded MPA systems. In doing so, we explored interactions between different sets of objectives, determined whether refinements to the existing spatial arrangement of MPAs were necessary, and tested the utility of existing MPAs by comparing their cost effectiveness with an MPA system designed from scratch. We found that MPAs in Brazil protect some aspects of coral reef biodiversity pattern (e.g. threatened fauna and ecosystem types more effectively than connectivity or resilience to global warming. Expanding the existing MPA system was as cost-effective as designing one from scratch only when multiple objectives were considered and management costs were accounted for. Our approach provides a comprehensive assessment of the benefits of integrating multiple objectives in the initial stages of conservation planning, and yields insights for planners of MPAs tackling multiple objectives in other regions.

Species of conservation concern and environmental stressors: Local regional and global effects [Chapter 6

Science.gov (United States)

Steven M. Ostoja; Mathew L. Brooks; Jeanne C. Chambers; Burton K. Pendleton

2013-01-01

Species conservation has traditionally been based on individual species within the context of their requisite habitat, which is generally defined as the communities and ecosystems deemed necessary for their persistence. Conservation decisions are hampered by the fact that environmental stressors that potentially threaten the persistence of species can operate at...

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

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Betty M Booker

2016-03-01

Full Text Available The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.

Introduction to Northeast Pacific Shark Biology, Ecology, and Conservation.

Science.gov (United States)

Lowry, Dayv; Larson, Shawn E

Sharks are iconic, sometimes apex, predators found in every ocean and, as a result, they have featured prominently in the mythology, history, and fisheries of diverse human cultures around the world. Because of their regional significance to fisheries and ecological role as predators, and as a result of concern over long-term stability of their populations, there has been an increasing amount of work focused on shark conservation in recent decades. This volume highlights the biodiversity and biological attributes of, and conservation efforts targeted at, populations of sharks that reside in the Northeast Pacific Ocean bordering the west coast of the United States and Canada, one of the most economically and ecologically important oceanic regions in the world. A companion volume addresses details of fisheries and ecotourism in the same region, as well as delving into the relationship between captive husbandry of sharks and education/outreach efforts aimed at fostering a conservation mindset in the public at large. Together, these volumes provide readers a detailed backdrop against which to consider their own actions, and those of resource managers, academics, and educators, as they relate to the long-term conservation of sharks and their relatives. © 2017 Elsevier Ltd. All rights reserved.

Conservation of Sand Dune Vegetation in Coastal areas of the Valencian Region (Spain); Estado de conservacion de la vegetacion dunar en las costas de la comunidad Valenciana

Energy Technology Data Exchange (ETDEWEB)

Albertos, B.; San Miguel, E.; Draper, I.; Garilleti, R.; Lara, F.; Varela, J. M.

2010-07-01

The state of conservation of the coastal dune vegetation in Valencia region has been assessed within a survey of the vegetal communities present in these systems.The conservation status has been evaluated through a qualitative scale which integrates criteria such as dune extension, structure and diversity of the vegetal communities, level of ruderalization, presence of invasive species, and floristic rarity. Special attention has been paid to the usual aggressions to this type of ecosystem and the situation of the most aggressive invasive plants. (Author) 15 refs.

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin e during eye development

KAUST Repository

Liu, Qingxin

2014-06-16

During Drosophila eye development, differentiation initiates in the posterior region of the eye disk and progresses anteriorly as a wave marked by the morphogenetic furrow (MF), which demarcates the boundary between anterior undifferentiated cells and posterior differentiated photoreceptors. However, the mechanism underlying the regulation of gene expression immediately before the onset of differentiation remains unclear. Here, we show that Apontic (Apt), which is an evolutionarily conserved transcription factor, is expressed in the differentiating cells posterior to the MF. Moreover, it directly induces the expression of cyclin E and is also required for the G1-to-S phase transition, which is known to be essential for the initiation of cell differentiation at the MF. These observations identify a pathway crucial for eye development, governed by a mechanism in which Cyclin E promotes the G1-to-S phase transition when regulated by Apt.

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin e during eye development

KAUST Repository

Liu, Qingxin; Wang, Xianfeng; Ikeo, Kazuho; Hirose, Susumu; Gehring, Walter Jakob; Gojobori, Takashi

2014-01-01

During Drosophila eye development, differentiation initiates in the posterior region of the eye disk and progresses anteriorly as a wave marked by the morphogenetic furrow (MF), which demarcates the boundary between anterior undifferentiated cells and posterior differentiated photoreceptors. However, the mechanism underlying the regulation of gene expression immediately before the onset of differentiation remains unclear. Here, we show that Apontic (Apt), which is an evolutionarily conserved transcription factor, is expressed in the differentiating cells posterior to the MF. Moreover, it directly induces the expression of cyclin E and is also required for the G1-to-S phase transition, which is known to be essential for the initiation of cell differentiation at the MF. These observations identify a pathway crucial for eye development, governed by a mechanism in which Cyclin E promotes the G1-to-S phase transition when regulated by Apt.

Variational formulation of relaxed and multi-region relaxed magnetohydrodynamics

Science.gov (United States)

Dewar, R. L.; Yoshida, Z.; Bhattacharjee, A.; Hudson, S. R.

2015-12-01

> Ideal magnetohydrodynamics (IMHD) is strongly constrained by an infinite number of microscopic constraints expressing mass, entropy and magnetic flux conservation in each infinitesimal fluid element, the latter preventing magnetic reconnection. By contrast, in the Taylor relaxation model for formation of macroscopically self-organized plasma equilibrium states, all these constraints are relaxed save for the global magnetic fluxes and helicity. A Lagrangian variational principle is presented that leads to a new, fully dynamical, relaxed magnetohydrodynamics (RxMHD), such that all static solutions are Taylor states but also allows state with flow. By postulating that some long-lived macroscopic current sheets can act as barriers to relaxation, separating the plasma into multiple relaxation regions, a further generalization, multi-region relaxed magnetohydrodynamics (MRxMHD) is developed.

Governance factors in the identification of global conservation priorities for mammals.

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Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

2011-09-27

Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development.

Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.

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Hodar, Christian; Zuñiga, Alejandro; Pulgar, Rodrigo; Travisany, Dante; Chacon, Carlos; Pino, Michael; Maass, Alejandro; Cambiazo, Verónica

2014-02-10

In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica. Copyright © 2013 Elsevier B.V. All rights reserved.

Is Ki-67 Expression Prognostic for Local Relapse in Early-Stage Breast Cancer Patients Treated With Breast Conservation Therapy (BCT)?

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Hafeez, Farhaan [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States); Neboori, Hanmanth J. [Drexel Medical College, Philadelphia, Pennsylvania (United States); Harigopal, Malini [Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (United States); Wu, Hao; Haffty, Bruce G. [Department of Radiation Oncology, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson School of Medicine, New Brunswick, New Jersey (United States); Yang, Qifeng [Department of Breast Surgery, Shandong University School of Medicine, Shanghai (China); Schiff, Devora [Department of Radiation Oncology, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson School of Medicine, New Brunswick, New Jersey (United States); Moran, Meena S., E-mail: meena.moran@yale.edu [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States)

2013-10-01

Purpose: Ki-67 is a human nuclear protein whose expression is strongly up-regulated in proliferating cells and can be used to determine the growth fraction in clonal cell populations. Although there are some data to suggest that Ki-67 overexpression may be prognostic for endpoints such as survival or postmastectomy recurrence, further elucidation of its prognostic significance is warranted. Specifically after breast conservation therapy (BCT) (defined in this setting as breast-conserving surgery and adjuvant radiation therapy), whether Ki-67 predicts for locoregional recurrence has not been investigated. The purpose of this study was to assess Ki-67 expression in a cohort of early-stage breast cancer patients to determine whether a significant independent association between Ki-67 and locoregional relapse exists. Methods and Materials: Ki-67 staining was conducted on a tissue microarray of 438 patients previously treated with BCT, and expression was analyzed with clinicopathologic features and outcomes from our database. Results: Ki-67 expression was more prevalent in black patients (37% of black patients vs 17% of white patients, P<.01), younger patients (27% of patients aged ≤50 years vs 15% of patients aged >50 years, P<.01), estrogen receptor (ER)–negative tumors (25% of ER-negative tumors vs 17% of ER-positive tumors, P=.04), human epidermal growth factor receptor 2 (HER2)/neu–positive tumors (35% of HER2-positive tumors vs 18% of HER2-negative tumors, P=.01), and larger tumors (26% of T2 tumors vs 16% of T1 tumors, P=.03). On univariate/multivariate analysis, Ki-67 did not predict for overall survival (74.4% vs 72.6%), cause-specific survival (82.9% vs 82.1%), local relapse-free survival (83.6% vs 88.5%), distant metastasis-free survival (76.1% vs 81.4%), recurrence-free survival (65.5% vs 74.6%), and locoregional recurrence-free survival (81.6% vs 84.7%): P>.05 for all. Conclusions: Ki-67 appears to be a surrogate marker for aggressive disease and

Differential conservation and divergence of fertility genes boule and dazl in the rainbow trout.

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Mingyou Li

Full Text Available BACKGROUND: The genes boule and dazl are members of the DAZ (Deleted in Azoospermia family encoding RNA binding proteins essential for germ cell development. Although dazl exhibits bisexual expression in mitotic and meiotic germ cells in diverse animals, boule shows unisexual meiotic expression in invertebrates and mammals but a bisexual mitotic and meiotic expression in medaka. How boule and dazl have evolved different expression patterns in diverse organisms has remained unknown. METHODOLOGY AND PRINCIPAL FINDINGS: Here we chose the fish rainbow trout (Oncorhynchus mykiss as a second lower vertebrate model to investigate the expression of boule and dazl. By molecular cloning and sequence comparison, we identified cDNAs encoding the trout Boule and Dazl proteins, which have a conserved RNA-recognition motif and a maximal similarity to their homologs. By RT-PCR analysis, adult RNA expression of trout boule and dazl is restricted to the gonads of both sexes. By chromogenic and two-color fluorescence in situ hybridization, we revealed bisexual and germline-specific expression of boule and dazl. We found that dazl displays conserved expression throughout gametogenesis and concentrates in the Balbinani's body of early oocytes and the chromatoid body of sperm. Surprisingly, boule exhibits mitotic and meiotic expression in the male but meiosis-specific expression in the female. CONCLUSIONS: Our data underscores differential conservation and divergence of DAZ family genes during vertebrate evolution. We propose a model in which the diversity of boule expression in sex and stage specificity might have resulted from selective loss or gain of its expression in one sex and mitotic germ cells.

Conservation laws shape dissipation

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Rao, Riccardo; Esposito, Massimiliano

2018-02-01

Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs—we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.

Selective constraint on noncoding regions of hominid genomes.

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Eliot C Bush

2005-12-01

Full Text Available An important challenge for human evolutionary biology is to understand the genetic basis of human-chimpanzee differences. One influential idea holds that such differences depend, to a large extent, on adaptive changes in gene expression. An important step in assessing this hypothesis involves gaining a better understanding of selective constraint on noncoding regions of hominid genomes. In noncoding sequence, functional elements are frequently small and can be separated by large nonfunctional regions. For this reason, constraint in hominid genomes is likely to be patchy. Here we use conservation in more distantly related mammals and amniotes as a way of identifying small sequence windows that are likely to be functional. We find that putatively functional noncoding elements defined in this manner are subject to significant selective constraint in hominids.

Selective Constraint on Noncoding Regions of Hominid Genomes.

Directory of Open Access Journals (Sweden)

2005-12-01

Full Text Available An important challenge for human evolutionary biology is to understand the genetic basis of human-chimpanzee differences. One influential idea holds that such differences depend, to a large extent, on adaptive changes in gene expression. An important step in assessing this hypothesis involves gaining a better understanding of selective constraint on noncoding regions of hominid genomes. In noncoding sequence, functional elements are frequently small and can be separated by large nonfunctional regions. For this reason, constraint in hominid genomes is likely to be patchy. Here we use conservation in more distantly related mammals and amniotes as a way of identifying small sequence windows that are likely to be functional. We find that putatively functional noncoding elements defined in this manner are subject to significant selective constraint in hominids.

Aligning conservation goals: are patterns of species richness and endemism concordant at regional scales?

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Ricketts, T. H.

2001-01-01

Full Text Available Biodiversity conservation strategies commonly target areas of high species richness and/or high endemism. However, the correlation between richness and endemism at scales relevant to conservation is unclear; these two common goals of conservation plans may therefore be in conflict. Here the spatial concordance between richness and endemism is tested using five taxa in North America: butterflies, birds, mammals, amphibians, and reptiles. This concordance is also tested using overall indices of richness and endemism (incorporating all five taxa. For all taxa except birds, richness and endemism were significantly correlated, with amphibians, reptiles, and the overall indices showing the highest correlations (rs = 0.527-0.676. However, 'priority sets' of ecoregions (i.e., the top 10% of ecoregions based on richness generally overlapped poorly with those based on endemism (< 50% overlap for all but reptiles. These results offer only limited support for the idea that richness and endemism are correlated at broad scales and indicate that land managers will need to balance these dual, and often conflicting, goals of biodiversity conservation.

Prioritizing land and sea conservation investments to protect coral reefs.

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Carissa J Klein

Full Text Available BACKGROUND: Coral reefs have exceptional biodiversity, support the livelihoods of millions of people, and are threatened by multiple human activities on land (e.g. farming and in the sea (e.g. overfishing. Most conservation efforts occur at local scales and, when effective, can increase the resilience of coral reefs to global threats such as climate change (e.g. warming water and ocean acidification. Limited resources for conservation require that we efficiently prioritize where and how to best sustain coral reef ecosystems. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop the first prioritization approach that can guide regional-scale conservation investments in land- and sea-based conservation actions that cost-effectively mitigate threats to coral reefs, and apply it to the Coral Triangle, an area of significant global attention and funding. Using information on threats to marine ecosystems, effectiveness of management actions at abating threats, and the management and opportunity costs of actions, we calculate the rate of return on investment in two conservation actions in sixteen ecoregions. We discover that marine conservation almost always trumps terrestrial conservation within any ecoregion, but terrestrial conservation in one ecoregion can be a better investment than marine conservation in another. We show how these results could be used to allocate a limited budget for conservation and compare them to priorities based on individual criteria. CONCLUSIONS/SIGNIFICANCE: Previous prioritization approaches do not consider both land and sea-based threats or the socioeconomic costs of conserving coral reefs. A simple and transparent approach like ours is essential to support effective coral reef conservation decisions in a large and diverse region like the Coral Triangle, but can be applied at any scale and to other marine ecosystems.

Assessment of the Ecosystem Services Capacity in Natural Protected Areas for Biodiversity Conservation

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Ronchi, Silvia; Salata, Stefano

2017-10-01

Recently, in Italy, a legislative proposal has been set to reform the role and the functions of natural protected areas promoting their aggregation (or the abolition) pursuing a better efficiency for their administration and economic saving. The system of natural protected areas is composed of different conservation levels: there are the Natural parks, established in the ‘80 by national or regional institution for the safeguard of natural elements, the Natura 2000 -Habitat 92/43/CEE promoted by European Union, with conservation measures for maintaining or restoring habitats and species of Communitarian interest, and the local parks of supra-municipal interest (namely PLIS) created by single municipalities or their aggregation aimed at limiting the soil sealing process. The hierarchical level of protection has determined differences in the management of the areas which leads to various approaches and strategies for biodiversity conservation and integrity. In order to assess strengths and weaknesses of the legislative initiative, the new management framework should be designed, considering the ecosystem characteristics of each natural protected area to define the future opportunities and critics, rather than, in the extreme case, remove the level of protection due to the absence of valuable ecosystem conditions. The paper provides an operative support to better apply the legislative proposal investigating the dynamics that affect all protected areas using the land take process as a major threat to biodiversity conservation in natural zones. The land take process is explored using the Land Use Change analysis (LUCa) as a possible way to determine the impact and the environmental effects of land transitions. LUCa is also useful to determine the loss of protected zones capacity to support Ecosystem Services. Finally, the assessment of the Ecosystem Services Capacity (ESC) index expresses the ability of each LULC to provide ES and, in particular, the Ecological

Re-expression of pro-fibrotic, embryonic preserved mediators in irradiated arterial vessels of the head and neck region.

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Möbius, Patrick; Preidl, Raimund H M; Weber, Manuel; Amann, Kerstin; Neukam, Friedrich W; Wehrhan, Falk

2017-11-01

Surgical treatment of head and neck malignancies frequently includes microvascular free tissue transfer. Preoperative radiotherapy increases postoperative fibrosis-related complications up to transplant loss. Fibrogenesis is associated with re-expression of embryonic preserved tissue developmental mediators: osteopontin (OPN), regulated by sex-determining region Y‑box 9 (Sox9), and homeobox A9 (HoxA9) play important roles in pathologic tissue remodeling and are upregulated in atherosclerotic vascular lesions; dickkopf-1 (DKK1) inhibits pro-fibrotic and atherogenic Wnt signaling. We evaluated the influence of irradiation on expression of these mediators in arteries of the head and neck region. DKK1, HoxA9, OPN, and Sox9 expression was examined immunohistochemically in 24 irradiated and 24 nonirradiated arteries of the lower head and neck region. The ratio of positive cells to total cell number (labeling index) in the investigated vessel walls was assessed semiquantitatively. DKK1 expression was significantly decreased, whereas HoxA9, OPN, and Sox9 expression were significantly increased in irradiated compared to nonirradiated arterial vessels. Preoperative radiotherapy induces re-expression of embryonic preserved mediators in arterial vessels and may thus contribute to enhanced activation of pro-fibrotic downstream signaling leading to media hypertrophy and intima degeneration comparable to fibrotic development steps in atherosclerosis. These histopathological changes may be promoted by HoxA9-, OPN-, and Sox9-related inflammation and vascular remodeling, supported by downregulation of anti-fibrotic DKK1. Future pharmaceutical strategies targeting these vessel alterations, e. g., bisphosphonates, might reduce postoperative complications in free tissue transfer.

Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei).

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Xi, Qian-Yun; Xiong, Yuan-Yan; Wang, Yuan-Mei; Cheng, Xiao; Qi, Qi-En; Shu, Gang; Wang, Song-Bo; Wang, Li-Na; Gao, Ping; Zhu, Xiao-Tong; Jiang, Qing-Yan; Zhang, Yong-Liang; Liu, Li

2015-01-01

Of late years, a large amount of conserved and species-specific microRNAs (miRNAs) have been performed on identification from species which are economically important but lack a full genome sequence. In this study, Solexa deep sequencing and cross-species miRNA microarray were used to detect miRNAs in white shrimp. We identified 239 conserved miRNAs, 14 miRNA* sequences and 20 novel miRNAs by bioinformatics analysis from 7,561,406 high-quality reads representing 325,370 distinct sequences. The all 20 novel miRNAs were species-specific in white shrimp and not homologous in other species. Using the conserved miRNAs from the miRBase database as a query set to search for homologs from shrimp expressed sequence tags (ESTs), 32 conserved computationally predicted miRNAs were discovered in shrimp. In addition, using microarray analysis in the shrimp fed with Panax ginseng polysaccharide complex, 151 conserved miRNAs were identified, 18 of which were significant up-expression, while 49 miRNAs were significant down-expression. In particular, qRT-PCR analysis was also performed for nine miRNAs in three shrimp tissues such as muscle, gill and hepatopancreas. Results showed that these miRNAs expression are tissue specific. Combining results of the three methods, we detected 20 novel and 394 conserved miRNAs. Verification with quantitative reverse transcription (qRT-PCR) and Northern blot showed a high confidentiality of data. The study provides the first comprehensive specific miRNA profile of white shrimp, which includes useful information for future investigations into the function of miRNAs in regulation of shrimp development and immunology.

Conservation of Charge and Conservation of Current

OpenAIRE

Eisenberg, Bob

2016-01-01

Conservation of current and conservation of charge are nearly the same thing: when enough is known about charge movement, conservation of current can be derived from conservation of charge, in ideal dielectrics, for example. Conservation of current is enforced implicitly in ideal dielectrics by theories that conserve charge. But charge movement in real materials like semiconductors or ionic solutions is never ideal. We present an apparently universal derivation of conservation of current and ...

Isolation and expression analysis of EcbZIP17 from different finger millet genotypes shows conserved nature of the gene.

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Chopperla, Ramakrishna; Singh, Sonam; Mohanty, Sasmita; Reddy, Nanja; Padaria, Jasdeep C; Solanke, Amolkumar U

2017-10-01

Basic leucine zipper (bZIP) transcription factors comprise one of the largest gene families in plants. They play a key role in almost every aspect of plant growth and development and also in biotic and abiotic stress tolerance. In this study, we report isolation and characterization of EcbZIP17 , a group B bZIP transcription factor from a climate smart cereal, finger millet ( Eleusine coracana L.). The genomic sequence of EcbZIP17 is 2662 bp long encompassing two exons and one intron with ORF of 1722 bp and peptide length of 573 aa. This gene is homologous to AtbZIP17 ( Arabidopsis ), ZmbZIP17 (maize) and OsbZIP60 (rice) which play a key role in endoplasmic reticulum (ER) stress pathway. In silico analysis confirmed the presence of basic leucine zipper (bZIP) and transmembrane (TM) domains in the EcbZIP17 protein. Allele mining of this gene in 16 different genotypes by Sanger sequencing revealed no variation in nucleotide sequence, including the 618 bp long intron. Expression analysis of EcbZIP17 under heat stress exhibited similar pattern of expression in all the genotypes across time intervals with highest upregulation after 4 h. The present study established the conserved nature of EcbZIP17 at nucleotide and expression level.

Evolving concepts and opportunities in soil conservation

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Julian Dumanski

2015-03-01

The paper discusses some of the new driving forces, new international programs, and new potential partners in soil conservation. Increasingly, international efforts to mitigate land degradation are shifting from studies of the biophysical processes to improving the global, national and local enabling policy environment, as well as mainstreaming of soil conservation into national and regional policies and programs. Also, increased emphasis is placed on economic instruments and international markets, such as carbon trading, and incorporation of non-market values in ecosystem investment, such as payment for ecosystem services, certification schemes, etc. The paper discusses some of the opportunities for soil conservation that accrue from these new driving forces.

The value of information in conservation planning: Selecting retention trees for lichen conservation

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Karin Perhans; Robert G. Haight; Lena Gustafsson

2014-01-01

Conservation planning studies at small scales such as forest stands and below are uncommon. However, for retention forestry, developed during the last two decades and with current wide and increasing application in boreal and temperate regions, the need for cost-effective selection of individual trees is evident. In retention forestry certain trees are left at final...

Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

Science.gov (United States)

Harraghy, Niamh; Homerova, Dagmar; Herrmann, Mathias; Kormanec, Jan

2008-01-01

Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

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

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Jagtap, Soham; Shivaprasad, Padubidri V

2014-12-02

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

FDG uptake and glut-1 expression in primary tumors and loco-regional lymph nodes in non-small-cell lung cancer

International Nuclear Information System (INIS)

Lee, Won Woo; Nguyen, Xuan Canh; Chung, Jin Haeng; Park, So Yeon; Kim, Sang Eun

2007-01-01

FDG uptake level by primary tumors in NSCLC may affect the likelihood of malignant involvement in loco-regional lymph nodes (LNs). FDG uptake in tumors has been reported to be mediated by glucose transporter type 1 (Glut-I). Here, we investigated the correlations between primary tumors and loco-regional LNs in NSCLC regarding FDG uptake and Glut-1 expression. 126 NSCLC patients (M: F=103: 23, age=659.7y) who underwent curative resection and loco-regional LN dissection within 4 week period after FDG-PET study were enrolled. Maximum standardized uptake value (maxSUV) by PET and %Glut-1 expression by immunostaining were compared between primary tumors and FDG uptake positive loco-regional LNs. Significant correlations were found between 52 malignant LNs and 37 primary tumors in terms of maxSUV (r=0.6451, p<0.0001) and %Glut-1 expression (r=0.8341, p<0.0001). Linear regression of the relation between maxSUVs of malignant LNs (Y) and maxSUVs of primary tumors (X) yielded the expression Y = 0.5938 + 0.4808 X with an r2 value of 0.4162. On the other hand, no significant correlation was observed between 144 benign LNs and 75 primary tumors in terms of maxSUVs (r= -0.0125, p 0.8831). Moreover, %Glut-1 expressions of pathologically proven benign LNs and primary tumors were found to be correlated (r=0.3863, p=0.0004), but r2 value was low at 0.1492. High correlations were found between primary tumors and loco-regional metastatic LNs in NSCLC regarding FDG uptake and Glut-1 expression. Mediastinal LN staging of NSCLC by FDG-PET may be improved by considering the linear correlation between FDG uptakes of metastatic LNs and primary tumors

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

Science.gov (United States)

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

2013-05-28

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.

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

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Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.; Salzberg, Steven L.; Rubin, Gerald M.; Eisen, Michael B.; Celniker, SusanE.

2004-08-06

The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function--such as binding-site clustering--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.

A regulatory code for neuron-specific odor receptor expression.

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Anandasankar Ray

2008-05-01

Full Text Available Olfactory receptor neurons (ORNs must select-from a large repertoire-which odor receptors to express. In Drosophila, most ORNs express one of 60 Or genes, and most Or genes are expressed in a single ORN class in a process that produces a stereotyped receptor-to-neuron map. The construction of this map poses a problem of receptor gene regulation that is remarkable in its dimension and about which little is known. By using a phylogenetic approach and the genome sequences of 12 Drosophila species, we systematically identified regulatory elements that are evolutionarily conserved and specific for individual Or genes of the maxillary palp. Genetic analysis of these elements supports a model in which each receptor gene contains a zip code, consisting of elements that act positively to promote expression in a subset of ORN classes, and elements that restrict expression to a single ORN class. We identified a transcription factor, Scalloped, that mediates repression. Some elements are used in other chemosensory organs, and some are conserved upstream of axon-guidance genes. Surprisingly, the odor response spectra and organization of maxillary palp ORNs have been extremely well-conserved for tens of millions of years, even though the amino acid sequences of the receptors are not highly conserved. These results, taken together, define the logic by which individual ORNs in the maxillary palp select which odor receptors to express.

A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons.

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Kensuke Tashiro

Full Text Available Short interspersed repetitive elements (SINEs are highly repeated sequences that account for a significant proportion of many eukaryotic genomes and are usually considered "junk DNA". However, we previously discovered that many AmnSINE1 loci are evolutionarily conserved across mammalian genomes, suggesting that they may have acquired significant functions involved in controlling mammalian-specific traits. Notably, we identified the AS021 SINE locus, located 390 kbp upstream of Satb2. Using transgenic mice, we showed that this SINE displays specific enhancer activity in the developing cerebral cortex. The transcription factor Satb2 is expressed by cortical neurons extending axons through the corpus callosum and is a determinant of callosal versus subcortical projection. Mouse mutants reveal a crucial function for Sabt2 in corpus callosum formation. In this study, we compared the enhancer activity of the AS021 locus with Satb2 expression during telencephalic development in the mouse. First, we showed that the AS021 enhancer is specifically activated in early-born Satb2(+ neurons. Second, we demonstrated that the activity of the AS021 enhancer recapitulates the expression of Satb2 at later embryonic and postnatal stages in deep-layer but not superficial-layer neurons, suggesting the possibility that the expression of Satb2 in these two subpopulations of cortical neurons is under genetically distinct transcriptional control. Third, we showed that the AS021 enhancer is activated in neurons projecting through the corpus callosum, as described for Satb2(+ neurons. Notably, AS021 drives specific expression in axons crossing through the ventral (TAG1(-/NPY(+ portion of the corpus callosum, confirming that it is active in a subpopulation of callosal neurons. These data suggest that exaptation of the AS021 SINE locus might be involved in enhancement of Satb2 expression, leading to the establishment of interhemispheric communication via the corpus callosum

The clinical impact of hypoxia-regulated gene expression in loco-regional gastroesophageal cancer

DEFF Research Database (Denmark)

Winther, M.; Alsner, J.; Tramm, T.

2015-01-01

Purpose/Objective: In a former study (1), the hypoxia gene expression classifier, developed in head and neck squamous cell carcinomas, was applied in 89 patients with loco-regional gastroesophageal cancer (GC). Analysis of the 15 genes was indicative of hypoxia being more profound in esophagus...... and display greater heterogeneity compared to AC. However, previous indications that the hypoxia classifier might hold prognostic significance in ESCC patients could not be confirmed. Ongoing work includes in vitro studies of esophageal cancer cell lines in order to identify alternative hypoxia induced genes...... and to further explore the prognostic value of hypoxia in patients with loco-regional gastroesophageal cancer. (Figure Presented)....

Developmental Regulation of Gonadotropin-releasing Hormone Gene Expression by the MSX and DLX Homeodomain Protein Families*

Science.gov (United States)

Givens, Marjory L.; Rave-Harel, Naama; Goonewardena, Vinodha D.; Kurotani, Reiko; Berdy, Sara E.; Swan, Christo H.; Rubenstein, John L. R.; Robert, Benoit; Mellon, Pamela L.

2010-01-01

Gonadotropin-releasing hormone (GnRH) is the central regulator of the hypothalamic-pituitary-gonadal axis, controlling sexual maturation and fertility in diverse species from fish to humans. GnRH gene expression is limited to a discrete population of neurons that migrate through the nasal region into the hypothalamus during embryonic development. The GnRH regulatory region contains four conserved homeodomain binding sites (ATTA) that are essential for basal promoter activity and cell-specific expression of the GnRH gene. MSX and DLX are members of the Antennapedia class of non-Hox homeodomain transcription factors that regulate gene expression and influence development of the craniofacial structures and anterior forebrain. Here, we report that expression patterns of the Msx and Dlx families of homeodomain transcription factors largely coincide with the migratory route of GnRH neurons and co-express with GnRH in neurons during embryonic development. In addition, MSX and DLX family members bind directly to the ATTA consensus sequences and regulate transcriptional activity of the GnRH promoter. Finally, mice lacking MSX1 or DLX1 and 2 show altered numbers of GnRH-expressing cells in regions where these factors likely function. These findings strongly support a role for MSX and DLX in contributing to spatiotemporal regulation of GnRH transcription during development. PMID:15743757

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

Science.gov (United States)

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

2014-06-01

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

Bird diversity in the Serra do Aracá region, northwestern Brazilian Amazon: preliminary check-list with considerations on biogeography and conservation

Directory of Open Access Journals (Sweden)

Sérgio Henrique Borges

2014-08-01

Full Text Available We inventoried the birds from Serra do Aracá region, state of Amazonas. The region encompasses a high diversity of vegetation types, including white sand forests and campinas, terra firme and flooded forests, montane forests and tepuis. We recorded 416 bird taxa in 69 families through captures with mist nets, tape recording of bird voices, and collection of voucher specimens. A large proportion of them (61% were recorded in a single vegetation type. Qualitative estimates suggest that approximately 580 bird species occur in the region. The avifauna of the Aracá region has a mixed biogeographic composition, with species typical of both margins of the Rio Negro occurring sympatrically. Additionally, species whose distributions are restricted to three areas of endemism for Amazonian birds (Imeri, Guiana and Pantepui were recorded in the region. Rare landscapes in the Brazilian Amazon are found in the Serra do Aracá region. Additionally, we recorded endemic and rare birds, highlighting the value of the region for conservation. The Serra do Aracá State Park officially protects montane forests, terra firme forests and tepuis. We suggest that the large extension of white sand campinas and igapó forests at the southern portion of Serra do Aracá should be also preserved in order to improve the representation of the rich natural heritage of the region.

A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury.

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Guenther, Catherine A; Wang, Zhen; Li, Emma; Tran, Misha C; Logan, Catriona Y; Nusse, Roel; Pantalena-Filho, Luiz; Yang, George P; Kingsley, David M

2015-08-01

Bone morphogenetic proteins (BMPs) are key signaling molecules required for normal development of bones and other tissues. Previous studies have shown that null mutations in the mouse Bmp5 gene alter the size, shape and number of multiple bone and cartilage structures during development. Bmp5 mutations also delay healing of rib fractures in adult mutants, suggesting that the same signals used to pattern embryonic bone and cartilage are also reused during skeletal regeneration and repair. Despite intense interest in BMPs as agents for stimulating bone formation in clinical applications, little is known about the regulatory elements that control developmental or injury-induced BMP expression. To compare the DNA sequences that activate gene expression during embryonic bone formation and following acute injuries in adult animals, we assayed regions surrounding the Bmp5 gene for their ability to stimulate lacZ reporter gene expression in transgenic mice. Multiple genomic fragments, distributed across the Bmp5 locus, collectively coordinate expression in discrete anatomic domains during normal development, including in embryonic ribs. In contrast, a distinct regulatory region activated expression following rib fracture in adult animals. The same injury control region triggered gene expression in mesenchymal cells following tibia fracture, in migrating keratinocytes following dorsal skin wounding, and in regenerating epithelial cells following lung injury. The Bmp5 gene thus contains an "injury response" control region that is distinct from embryonic enhancers, and that is activated by multiple types of injury in adult animals. Copyright © 2015 Elsevier Inc. All rights reserved.

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

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Patterson, Tamatha A.; Grundel, Ralph

2014-01-01

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

Isolation, characterization, and expression of Le-msx, a maternally expressed member of the msx gene family from the glossiphoniid leech, Helobdella.

Science.gov (United States)

Master, V A; Kourakis, M J; Martindale, M Q

1996-12-01

The msx gene family is one of the most highly conserved of the nonclustered homeobox-containing genes. We have isolated an msx homolog (Le-msx) from the glossiphoniid leech, Helobdella robusta, and characterized its pattern of expression by whole mount in situ hybridization. In situ expression and reverse transcription polymerase chain reaction (RT-PCR) data results show that Le-msx is a maternal transcript initially uniformly distributed in the cortex of immature oocytes that becomes asymmetrically localized to the polar regions of the uncleaved zygote. This is the earliest reported expression for the msx gene family and the first maternally expressed homeodomain-containing transcription factor reported in annelids. During embryonic development, Le-msx is expressed in all 10 embryonic stem cells and their segmental founder cell descendants. At midembryonic stages, Le-msx is expressed in the expanding germinal plate. Le-msx is confined to the central nervous system and nephridia at late (stage 9) stages and subsequently disappears from nephridia. In addition, we present a phylogenetic hypothesis for the evolution of the msx gene family, including the identification of a putative C. elegans msx homolog and the realignment of the sponge msx homolog to the NK class of homeodomain genes.

Tilapia and human CLIC2 structures are highly conserved.

Science.gov (United States)

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

2018-01-08

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

A highly conserved phenylalanine in the alpha, beta-T cell receptor (TCR) constant region determines the integrity of TCR/CD3 complexes

DEFF Research Database (Denmark)

Caspar-Bauguil, S; Arnaud, J; Huchenq, A

1994-01-01

In the present study, we have investigated the importance of a phenylalanine (phe195) in the Tcr-C alpha region on Tcr-alpha,beta/CD3 membrane expression. An exchange of phe195 with a tyrosine residue does not affect Tcr/CD3 membrane expression; however, exchange with aspartic acid, histidine or ...

Two estrogen response element sequences near the PCNA gene are not responsible for its estrogen-enhanced expression in MCF7 cells.

Science.gov (United States)

Wang, Cheng; Yu, Jie; Kallen, Caleb B

2008-01-01

The proliferating cell nuclear antigen (PCNA) is an essential component of DNA replication, cell cycle regulation, and epigenetic inheritance. High expression of PCNA is associated with poor prognosis in patients with breast cancer. The 5'-region of the PCNA gene contains two computationally-detected estrogen response element (ERE) sequences, one of which is evolutionarily conserved. Both of these sequences are of undocumented cis-regulatory function. We recently demonstrated that estradiol (E2) enhances PCNA mRNA expression in MCF7 breast cancer cells. MCF7 cells proliferate in response to E2. Here, we demonstrate that E2 rapidly enhanced PCNA mRNA and protein expression in a process that requires ERalpha as well as de novo protein synthesis. One of the two upstream ERE sequences was specifically bound by ERalpha-containing protein complexes, in vitro, in gel shift analysis. Yet, each ERE sequence, when cloned as a single copy, or when engineered as two tandem copies of the ERE-containing sequence, was not capable of activating a luciferase reporter construct in response to E2. In MCF7 cells, neither ERE-containing genomic region demonstrated E2-dependent recruitment of ERalpha by sensitive ChIP-PCR assays. We conclude that E2 enhances PCNA gene expression by an indirect process and that computational detection of EREs, even when evolutionarily conserved and when near E2-responsive genes, requires biochemical validation.