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CDNA library from the Latex of Hevea brasiliensis

CDNA library from the Latex of Hevea brasiliensis

Latex from Hevea brasiliensis contains 30-50% (w/w) of natural rubber (cis-1,4-polyisoprene), the important raw material for many rubber industries. We have constructed a cDNA library from the latex of H. brasiliensis to investigate the expressed genes and molecular events in the latex. We analyzed 412 expressed sequence tags (ESTs). More than 90% of the EST clones showed homology to previously described sequences in public databases. Functional classification of the ESTs showed that the largest category were proteins of unknown function (30.1%), 11.4% of ESTs encoded for rubber synthesis- related proteins (RS) and 8.5% for defense or stress related proteins (DS). Those with no significant homology to known sequences (NSH) accounted for 8.7%, primary metabolism (PM) and gene expression and RNA metabolism were 7.8% and 6.6%, respectively. Other categories included, protein synthesis-related proteins (6.6%), chromatin and DNA metabolism (CDM 3.9%), energy metabolism (EM 3.4%), cellular transport (CT 3.2%), cell structure (CS 3.2%), signal transduction (ST 2.2%), secondary metabolism (SM 1.7%), protein fate (PF 2.2%), and reproductive proteins (RP 0.7%).
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Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L.

Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L.

Total RNA was isolated by an improved CTAB method [54], and equal amounts of total RNA sampled at different time points were mixed to construct a full-length normalized cDNA library. Purification of mRNA from total RNA was carried out using the FastTrackH 2.0 Kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. cDNAs were synthesized using the Superscript Full-length Library Construction Kit II (Invitrogen) according to the manufacturers’ protocols, cloned into a Gateway pDONR222 vector (Invitrogen) by the BP cloning process, and transformed into Escherichia coli strain DH10B competent cells (Invitrogen) through electroporation using an E. coli Pulser (BTX Harvard Apparatus, Holliston, MA, USA). After the full-length library was constructed, plasmid DNA was extracted with the PureLink TM HQ Mini Plasmid DNA Purification Kit (Invitrogen). Normalization was per- formed by saturation hybridization between genomic DNA and mixed plasmid DNA from the cDNA library [55]. Then, clones were randomly selected and fully sequenced to test fullness ratios of the cDNA inserts of the library. Putative full-length cDNA sequences were identified by comparison with all available ORF- complete mRNA sequences from the NCBI nr protein database [56]. Finally, qRT-PCR was used to estimate the relative concentration of a highly abundant clone in both the non- normalized and the normalized cDNA populations.
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Gene expression analysis by ESTs sequencing of the Brazilian frog Phyllomedusa nordestina skin glands

Gene expression analysis by ESTs sequencing of the Brazilian frog Phyllomedusa nordestina skin glands

The first molecule belonging to the class of protease inhibitors was isolated from the skin of Bombina bombina, and it was shown to be a trypsin inhibitor named bomb- inina. Thereafter, several other inhibitors from the skin of Rana and Phyllomedusa were described, indicating that these protease inhibitors may contribute to the broad spectrum of antimicrobial activity in frog skin secretion (Gebhard et al., 2004). From the present P. nordestina cDNA library, we identify nine sequences belonging to the class of protease inhibitors. Seven of these sequences were group- ed in a contig named PI01, while other two sequences remained as singlets named PI02 and PI03. All clusters showed only a significant similarity by BlastX analysis, in which contig PI01 was shown to be 72% similar to protein PSKP1 isolated from P. sauvagii (GenBank ID:P83578.1). PSKP1 is a Kazal-type protein, but unlike Kazal, this protein is not an inhibitor of trypsin, chymotrypsin, S. aureus strain V8 protease or proteinase K, due to the presence of a Pro residue at position P 2 of the peptide. A Pro residue at this
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Cloning and characterization of a V-ATPase subunit C from the American visceral leishmaniasis vector Lutzomyia longipalpis modulated during development and blood ingestion

Cloning and characterization of a V-ATPase subunit C from the American visceral leishmaniasis vector Lutzomyia longipalpis modulated during development and blood ingestion

Visceral leishmaniasis (VL) is a serious tropical disease that affects approximately 500 thousand people worldwide every year. In the Americas, VL is caused by the parasite Leishmania (Leishmania) infantum chagasi mainly transmitted by the bite of the sand fly vector Lutzomyia longipalpis. Despite recent advances in the study of interaction between Leishmania and sand flies, very little is known about sand fly protein expression pro- files. Understanding how the expression of proteins may be affected by blood feeding and/or presence of para- site in the vector’s midgut might allow us to devise new strategies for controlling the spread of leishmaniasis. In this work, we report the characterization of a vacuolar ATPase subunit C from L. longipalpis by screening of a midgut cDNA library with a 220 bp fragment identified by means of differential display reverse transcriptase- polymerase chain reaction analysis. The expression of the gene varies along insect development and is upregulated in males and bloodfed L. longipalpis, compared to unfed flies.
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Functional characterization of chemosensory proteins in the scarab beetle, Holotrichia oblita Faldermann (Coleoptera: Scarabaeida).

Functional characterization of chemosensory proteins in the scarab beetle, Holotrichia oblita Faldermann (Coleoptera: Scarabaeida).

3 Construction of an H. oblita antennae cDNA library Total RNA from 100 female antennae was extracted with Trizol (Invitrogen, USA). Full-length double-stranded cDNA (ds cDNA) with blunt cDNA ends was synthesized and amplified using the Creator TM SMART TM cDNA Library Construction Kit (Clontech, USA). Synthesized ds cDNA was then incubated with 0.08 m g/ m l proteinase K at 45 uC for 20 min to inactivate the DNA polymerase. After size fractionation using CHROMA SPIN TM columns, the cDNA was incorporated into SfiI-digested lTripIE vector. The recombinant phage vector was transduced into E. coli XL1-Blue (TaKaRa Co., China). The plaques were counted to calculate the phage titer (pfu/ml), and the recombination efficiency was estimated by calculating the ratio of white (recombinant) to blue (non-recombinant) plaques. Fragments . 350 bp were sequenced.
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Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi

Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi

(P < 0.05). This result was expected considering that this caste executes the feeding of the colony, and it was consistent with a previous study conducted with Reticulitermes flavipes that found high levels of expression of this cellulase in workers, nymphs, alates and supplementary reproductives (Scharf et al., 2005). The β-glucosidase gene is similar to another homolog, the Neofem 2, which is believed to play a role in reproductive suppression in the termite, Cryptotermes secundus (Weil et al., 2007). A knockdown of Neofem 2 was conducted in queens, making the workers believe that the colony was queenless (Korb et al., 2009). Nevertheless, our experiments show that, in C. gestroi, the expression of this gene is extremely low in queens, supporting the idea that this enzyme works together with others to efficiently degrade cellulose. Earlier RT-PCR experiments demonstrate that workers of the lower termite, Neotermes koshunensis, are known to express β-glucosidase in the salivary glands (Tokuda et al., 2002), supporting our findings since we generated a cDNA library from workers’ heads. A differential study of the digestive cellulase expression among castes in two termite species showed that minor workers of Nasutitermes takasagoensis presented higher rates of expression of β-glucosidase, when compared to soldiers, medium and major workers, revealing a division of labor controlled by nutrition (Fujita et al., 2008). Even though the rates were differentially expressed, the site of expression was higher in the midgut for all castes. In the termite Hodotermopsis sjostesti, however, the expression was higher in the salivary glands for the worker caste and in the hindgut for the soldiers (Fujita et al., 2008). Further investi- gation are been carried out to locate the sites of expression of these cellulases in C. gestroi.
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Transcriptome analysis of the gilthead sea bream (sparus auratus) pituitary gland. Type I markers for molecular genetics

Transcriptome analysis of the gilthead sea bream (sparus auratus) pituitary gland. Type I markers for molecular genetics

The pituitary gland of vertebrates produces a number of hormones, growth hormone (GH), prolactin (PRL), somatolactin (SL), gonadotrophin (GTH), thyroid stimulating hormone (TSH), and proopiomelanocorticotrophin (POMC), which regulate a range of important production traits. In the present study a gilthead sea bream (Sparus auratus) pituitary cDNA library was arrayed (948 clones) in 96 well plates and used to generate expressed sequence tags (ESTs) for pituitary hormones and novel pituitary transcripts. Using a combination of colony blotting and sequencing 750 clones were analysed, 61 ESTs were isolated for the first time in Sparus auratus, 12 ESTs were identified for the first time in teleosts and 70 ESTs which corresponded to 58 genes were unidentified. In addition to isolating ESTs for all the pituitary hormones, four novel transcripts with high levels of expression in the pituitary gland were also identified. The present data contribute to an ongoing European project (Bridgemap, www.bridgemap.tuc.gr) which aims to generate molecular resources for implementation of a selective breeding program for gilthead sea bream in Europe.
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Estrutura populacional de Anopheles darlingi em diferentes localidades de Rondônia ao longo do Rio Madeira através da genotipagem de microssatélites

Estrutura populacional de Anopheles darlingi em diferentes localidades de Rondônia ao longo do Rio Madeira através da genotipagem de microssatélites

>gi|82560787|gb|DV729726.1|DV729726 ADM-P8-G10 Adult female salivary gland cDNA library Adarg1 Anopheles darlingi cDNA, mRNA sequence. AAACCTTAATTGATTGTGCATCAAGATGGAACTGACTGGCACAAGNA[r]

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Analysis and chromosomal mapping of Leishmania (Leishmania) amazonensis amastigote expressed sequence tags

Analysis and chromosomal mapping of Leishmania (Leishmania) amazonensis amastigote expressed sequence tags

The characterization of expressed sequence tags (ESTs) generated from a cDNA library of Leishmania (Leish- mania) amazonensis amastigotes is described. The sequencing of 93 clones generated new L. (L.) amazonensis ESTs from which 32% are not related to any other sequences in database and 68% presented significant simi- larities to known genes. The chromosome localization of some L. (L.) amazonensis ESTs was also determined in L. (L.) amazonensis and L. (L.) major. The characterization of these ESTs is suitable for the genome physical mapping, as well as for the identification of genes encoding cysteine proteinases implicated with protective immune responses in leishmaniasis.
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Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings

Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings

A full-length cDNA clone encoding cyclophilin gene of 848 bp, including a 519 bp open reading frame, has been isolated from the cDNA library constructed from etiolated seedlings of Vigna mungo (GenBank FN668732). The cDNA sequence showed 97% identity with Vigna radiata cyclophilin mRNA. The sequence was GC rich and lacked introns. The open reading frame encoded 172 amino acid polypeptide with molecular weight 18.3 kDa and theoretical pI 8.61. BlastP analysis indicated that its putative amino acid sequence shared 100% identity with several plant cyclophilins particularly legumes. The conserved seven amino acid residues region in V. mungo cyclophilin was RSGKPLH (present in legumes) instead of KSGKPLH, indicating its similarity to the cyclophilins of other legumes. This novel V. mungo cyclophilin gene will broaden the pool of plant cyclophilin genes for further studies.
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ABSTRACT: The phospholipase A2 superfamily encompasses 15 groups that are

ABSTRACT: The phospholipase A2 superfamily encompasses 15 groups that are

For the construction of the venom gland cDNA library, a pair of glands was excised from a male adult specimen of Crotalus durissus cascavella (2 kg weight and 125 cm length – measured from rostrum to cloaca) captured in Cabaceira, Paraíba state, Brazil, and maintained from 1999 to 2006 in the Laboratory of Venomous Animals and Toxins (LAPTOX), Federal University of Pernambuco, Recife state, Brazil. The snake venom was extracted by standard procedures three days before the surgery for gland excision, with the aim of reaching the maximal level of RNA synthesis. Once surgically removed, the venom glands were kept at –80°C until the procedures for RNA purification and analysis.
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Barriers Approach to Innovation in Academic Libraries

Barriers Approach to Innovation in Academic Libraries

With the rapid changes in the economic, political, social and technological environments, as well as the changes of higher education environments, academic libraries have undergone an extremely high pressure for innovation, thus are in need of adjustments on existing services and developments of new services, for dealing with challenges of management eficiencies and competitive advantages in an ever-changing world. This study focused on investigating academic library innovations from the organization framework, without discussions on individual creativity or technological innovation.
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Digital Library Activities in Europe: A Brief Overview

Digital Library Activities in Europe: A Brief Overview

Initially the writer intended to do her best to draw a panorama of the digital library activities in Europe. Unfortunately the thought was found to be too unrealistic to be realized not long after the work on the article began because of certain limitations, such as some original materials are not accessible in the networked environment. In a sense the influence of a digital library project is closely related to availability of the informa- tion resources on it. In addition the problem related to language is always one that troubles the writer. There is even no version of some projects in English which is the most common language in the scientific world. The problems might have troubled nu- merous researchers and practicians. Hopefully the development of the digital library could be also useful to solving some problems in the near future.
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World heritage digital library in Portugal: the convent of the order of Christ and the castle of the order of the temple

World heritage digital library in Portugal: the convent of the order of Christ and the castle of the order of the temple

Also, thinking about tourism, we can associate to the monasteries route different packages of cultural and environmental touring. For example, from an advanced search on the digital library, it can be selected a theme that enable the visitor to prepare a personalized tour. Again as an example, we have themes related to the Orders of Templars, Christ and Cister, architectural, artistic and scientific, and also relating to personalities so important as Henry the Navigator, or Pedro and Ines and their tragic love story.

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Between Library and Research Centre:  Metadata and Criticism

Between Library and Research Centre: Metadata and Criticism

Centred at first on the analysis of the role played by libraries, mainly the academic ones, in the process of canon-formation (described in the paper presented to The Tenth International Conference on the Book, held in 2012, in Barcelona, and already published in The International Journal of the Book, vol. 10, 2013), our research has had, from its very beginning, an objective much similar to the one claimed by Stephen Ramsay, in 2010, for the Emory University Centre for Digital Humanities as emphasised above – scholars and librarians working together, each of them as a librarian and a scholar, simultaneously. This was the main argument for choosing The International Library of Famous Literature, edited by Richard Garnett, and published in London, in 1899, as our first case study. This librarian of the British Museum was, at the same time, a respected scholar doing translations from different languages – Greek, German, Italian, Spanish, and Portuguese – producing biographies and studies of different authors, and writing poetry. Indeed, this close relation to be established between scholars and librarians, in our case between the Library of Faculdade de Letras da Universidade de Lisboa (LFLUL) and the University of Lisbon Centre for English Studies (ULICES), constitutes the very nexus of the title of this article – “Between Library and Research Centre: Metadata and Criticism.”
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Evaluation of library collections and the hybrid library

Evaluation of library collections and the hybrid library

Mednarodna organizacija IFLA (Poll, 1996) je izbrala 17 kazalcev, ki so namenje­ ni merjenju uspešnosti delovanja visokošolskih knjižnic, mednarodna zveza  za standardizacijo ISO pa 29 k[r]

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Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition.

Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition.

The ‘‘DNA/RNA binding, transcription and translation’’ category was the most abundant among the genes identified in the forward library, especially those that encode ribosomal proteins, taking over nearly half of the sequenced clones (342 ESTs). In addition, four unigenes individually encoded proteins homologous to transcription factor BTF3, retrotransposon protein, RNA helicase, and elongation factor 1-alpha. Previous studies confirmed that some ribosomal protein genes are regulated by different stress environments, including high salinity and cold stress [36,44,45]. Organisms have evolved a translation machinery referred to as de novo protein synthesis to cope with stress. In Chlorella, the increase in the number of transcripts of various ribosomal protein subunits may be responsible for the reboot of the photosynthetic apparatus and related enzymes after they are returned under light. In higher plants, transcription factor BTF3 is required for RNA polymerase II-dependent transcription. The downregulation of BTF3 expression reduces the chloroplast size and the chlorophyll content [46]. Therefore, the upregulation of BTF3 activity may contribute to chloroplast development in Chlorella to accommodate light stress. Plant retrotransposons are reportedly minimized by maintaining a quiescent state during normal growth and development but could be stress-induced under life-threatening situations [47]. Although the function of retrotransposon proteins in trophic transition remains unclear, the transcriptional increase may reflect a survival strategy in Chlorella during the transition from heterotrophy to photoautotrophy. RNA helicases are ubiquitous enzymes that function as molecular motors that rearrange duplex RNA secondary structures [48]. The helicases might be involved in regulating plant growth and development under stress conditions by regulating some stress- induced pathways [49,50]. In the present study, the mRNA induction of RNA helicase in the forward library may act as a potential regulator that buffers the sudden shock under glucose starvation and light stress. Two other ESTs that individually encode transposase (RYG263) and eukaryotic initiation factor 3e (RYG195) were found in the reverse library, despite the relationships between the two genes and heterotrophic growth have not yet been reported.
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Indexação automática e ontologias: identificação dos contributos convergentes na ciência da informação

Indexação automática e ontologias: identificação dos contributos convergentes na ciência da informação

Automatic and traditional indexing has always been a concern of the area of Information Science (IS). The lack of consistency in human indexing, and the lack of semantics in the automatic are regarded as major disadvantages. One possibility of providing computational systems with greater inference power is the use of ontologies. This proposal aims to identify and analyse studies in the area of IS that address the contributions of ontologies in automatic indexing. It is intended to (i) identify the scientific works, in the scientific journal databases of Library & Information Science, and Information Science & Technology Abstracts that approach this subject, its temporal and geographical distribution; (ii) identify and describe the centrality of the subject approach to the two concepts (automatic indexing and ontologies), and the methodological approach of the respective articles; (iii) identify the contributions present in the articles that make up the corpus regarding the potentialities of the joint use of the two concepts. It was based on an exploratory study based on a systematic review of the literature. The results show the contributions of the ontologies in the automatic indexing, such as: (i) disambiguation of homographs and ambiguous terms; (ii) greater ability to integrate semantic relationships in an automated way; (iii) a navigation and expansion of queries through semantic relationships; (iv) a more accurate and exhaustive retrieval of information. We conclude that the development of systems that use ontologies in its full potential in automatic indexing seek to overcome their lack of semantic capacity. Despite the promising results in this regard, it may be still a little early to speak of effective semantic indexing.
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A growth hormone-based phylogenetic analysis of euteleostean fishes including a representative species of the Atheriniformes Order, Odontesthes argentinensis

A growth hormone-based phylogenetic analysis of euteleostean fishes including a representative species of the Atheriniformes Order, Odontesthes argentinensis

The authors are grateful to Professor Norman Maclean for his helpful suggestions and Dr. Olga Francino for fruitful discussions. We also thank Rodrigo Maggioni for technical assistance with cDNA sequencing and Dr. Arati Iyengar for her careful reading of the manuscript. This research was partially supported by IFS (International Foundation for Science, Stockholm, Sweden) through a grant to L.F. Marins (Research Grant Agreement No. A/2915-1), CAPES (Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil), UAB (Universitat Autònoma de Barcelona, Spain) and FURG (Fundação Universidade Fe- deral do Rio Grande, Brazil).
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