Relevant bibliographies by topics / Sequence tar

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Academic literature on the topic 'Sequence tar'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Sequence tar"

1

Tsubouchi, Taishi, Yasuhiro Shimane, Keiko Usui, et al. "Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment." International Journal of Systematic and Evolutionary Microbiology 63, Pt_6 (2013): 1987–94. http://dx.doi.org/10.1099/ijs.0.043364-0.

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A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001T, was isolated from deep-sea floor sediment in Japan. Cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. Colonies were glossy, viscous and yellowish-white in colour. The temperature, pH and salt concentration range for growth were 2–41 °C, pH 6.5–10.0 and 1–4 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-001T belongs to the family Caulobacteraceae of the class Alphaproteobacteria , and lies between the genus Brevundimonas and the genus Caulobacter . Levels of similarity between the 16S rRNA gene sequence of strain TAR-001T and those of the type strains of Brevundimonas species were 93.3–95.7 %; highest sequence similarity was with the type strain of Brevundimonas diminuta . Levels of sequence similarity between those of the type strains of Caulobacter species were 94.9–96.0 %; highest sequence similarity was with the type strain of Caulobacter mirabilis . The G+C content of strain TAR-001T was 67.6 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol suggests strain TAR-001T is more closely to the genus Brevundimonas than to the genus Caulobacter . The mean DNA–DNA hybridization levels between strain TAR-001T and the type strains of two species of the genus Brevundimonas were higher than that of the genus Caulobacter . On the basis of polyphasic biological features and the 16S rRNA gene sequence comparison presented here, strain TAR-001T is considered to represent a novel species of the genus Brevundimonas , for which the name Brevundimonas abyssalis sp. nov. is proposed; the type strain is TAR-001T ( = JCM 18150T = CECT 8073T).
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Tsubouchi, Taishi, Sumihiro Koyama, Kozue Mori, et al. "Brevundimonas denitrificans sp. nov., a denitrifying bacterium isolated from deep subseafloor sediment." International Journal of Systematic and Evolutionary Microbiology 64, Pt_11 (2014): 3709–16. http://dx.doi.org/10.1099/ijs.0.067199-0.

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A novel Gram-stain-negative, aerobic, heterotrophic, stalked and capsulated bacterium with potential denitrification ability, designated strain TAR-002T, was isolated from deep seafloor sediment in Japan. Colonies lacked lustre, and were viscous and translucent white. The ranges of temperature, pH and salt concentration for growth were 8–30 °C, pH 6.0–10.0 and 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-002T belongs to the genus Brevundimonas of the class Alphaproteobacteria . Levels of similarity between the 16S rRNA gene sequence of strain TAR-002T and those of the type strains of species of the genus Brevundimonas were 93.5–98.9 %; the most closely related species was Brevundimonas basaltis . In DNA–DNA hybridization assays between strain TAR-002T and its phylogenetic neighbours, Brevundimonas lenta DS-18T, B. basaltis J22T, Brevundimonas subvibrioides ATCC 15264T and Brevundimonas alba DSM 4736T, mean hybridization levels were 6.4–27.7 %. The G+C content of strain TAR-002T was 70.3 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol (DGL) indicates the affiliation of strain TAR-002T with the genus Brevundimonas . On the basis of biological characteristics and 16S rRNA gene sequence comparisons, strain TAR-002T is considered to represent a novel species of the genus Brevundimonas , for which the name Brevundimonas denitrificans sp. nov. is proposed; the type strain is TAR-002T ( = NBRC 110107T = CECT 8537T).
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Brachner, Claudia, Vicky Fasen, and Alexander Lindner. "Extremes of autoregressive threshold processes." Advances in Applied Probability 41, no. 02 (2009): 428–51. http://dx.doi.org/10.1017/s0001867800003360.

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In this paper we study the tail and the extremal behaviors of stationary solutions of threshold autoregressive (TAR) models. It is shown that a regularly varying noise sequence leads in general to only an O-regularly varying tail of the stationary solution. Under further conditions on the partition, it is shown however that TAR(S,1) models of order 1 with S regimes have regularly varying tails, provided that the noise sequence is regularly varying. In these cases, the finite-dimensional distribution of the stationary solution is even multivariate regularly varying and its extremal behavior is studied via point process convergence. In particular, a TAR model with regularly varying noise can exhibit extremal clusters. This is in contrast to TAR models with noise in the maximum domain of attraction of the Gumbel distribution and which is either subexponential or in ℒ(γ) with γ > 0. In this case it turns out that the tail of the stationary solution behaves like a constant times that of the noise sequence, regardless of the order and the specific partition of the TAR model, and that the process cannot exhibit clusters on high levels.
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Brachner, Claudia, Vicky Fasen, and Alexander Lindner. "Extremes of autoregressive threshold processes." Advances in Applied Probability 41, no. 2 (2009): 428–51. http://dx.doi.org/10.1239/aap/1246886618.

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In this paper we study the tail and the extremal behaviors of stationary solutions of threshold autoregressive (TAR) models. It is shown that a regularly varying noise sequence leads in general to only an O-regularly varying tail of the stationary solution. Under further conditions on the partition, it is shown however that TAR(S,1) models of order 1 with S regimes have regularly varying tails, provided that the noise sequence is regularly varying. In these cases, the finite-dimensional distribution of the stationary solution is even multivariate regularly varying and its extremal behavior is studied via point process convergence. In particular, a TAR model with regularly varying noise can exhibit extremal clusters. This is in contrast to TAR models with noise in the maximum domain of attraction of the Gumbel distribution and which is either subexponential or in ℒ(γ) with γ > 0. In this case it turns out that the tail of the stationary solution behaves like a constant times that of the noise sequence, regardless of the order and the specific partition of the TAR model, and that the process cannot exhibit clusters on high levels.
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Sethaphong, Latsavongsakda, Abhishek Singh, Ashley E. Marlowe, and Yaroslava G. Yingling. "The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution." Journal of Physical Chemistry C 114, no. 12 (2010): 5506–12. http://dx.doi.org/10.1021/jp906147q.

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Feng, Sandy, and Eric C. Holland. "HIV-1 tat trans-activation requires the loop sequence within tar." Nature 334, no. 6178 (1988): 165–67. http://dx.doi.org/10.1038/334165a0.

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Okumura, Hisashi, So-ichiro Nishiyama, Akie Sasaki, Michio Homma, and Ikuro Kawagishi. "Chemotactic Adaptation Is Altered by Changes in the Carboxy-Terminal Sequence Conserved among the Major Methyl-Accepting Chemoreceptors." Journal of Bacteriology 180, no. 7 (1998): 1862–68. http://dx.doi.org/10.1128/jb.180.7.1862-1868.1998.

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ABSTRACT In Escherichia coli and Salmonella typhimurium, methylation and demethylation of receptors are responsible for chemotactic adaptation and are catalyzed by the methyltransferase CheR and the methylesterase CheB, respectively. Among the chemoreceptors of these species, Tsr, Tar, and Tcp have a well-conserved carboxy-terminal motif (NWET/SF) that is absent in Trg and Tap. When they are expressed as sole chemoreceptors, Tsr, Tar, and Tcp support good adaptation, but Trg and Tap are poorly methylated and supported only weak adaptation. It was recently discovered that CheR binds to the NWETF sequence of Tsr in vitro. To examine the physiological significance of this binding, we characterized mutant receptors in which this pentapeptide sequence was altered. C-terminally-mutated Tar and Tcp expressed in a receptorless E. coli strain mediated responses to aspartate and citrate, respectively, but their adaptation abilities were severely impaired. Their expression levels and attractant-sensing abilities were similar to those of the wild-type receptors, but the methylation levels of the mutant receptors increased only slightly upon addition of attractants. When CheR was overproduced, both the adaptation and methylation profiles of the mutant Tar receptor became comparable to those of wild-type Tar. Furthermore, overproduction of CheR also enhanced adaptive methylation of wild-type Trg, which lacks the NWETF sequence, in the absence of any other chemoreceptor. These results suggest that the pentapeptide sequence facilitates effective adaptation and methylation by recruiting CheR.
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Stunnenberg, Melissa, John L. van Hamme, Atze T. Das, Ben Berkhout, and Teunis B. H. Geijtenbeek. "Variations in the Abortive HIV-1 RNA Hairpin Do Not Impede Viral Sensing and Innate Immune Responses." Pathogens 10, no. 7 (2021): 897. http://dx.doi.org/10.3390/pathogens10070897.

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The highly conserved trans-acting response element (TAR) present in the RNA genome of human immunodeficiency virus 1 (HIV-1) is a stably folded hairpin structure involved in viral replication. However, TAR is also sensed by viral sensors, leading to antiviral immunity. While high variation in the TAR RNA structure renders the virus replication-incompetent, effects on viral sensing remain unclear. Here, we investigated the role of TAR RNA structure and stability on viral sensing. TAR mutants with deletions in the TAR hairpin that enhanced thermodynamic stability increased antiviral responses. Strikingly, TAR mutants with lower stability due to destabilization of the TAR hairpin also increased antiviral responses without affecting pro-inflammatory responses. Moreover, mutations that affected the TAR RNA sequence also enhanced specific antiviral responses. Our data suggest that mutations in TAR of replication-incompetent viruses can still induce immune responses via viral sensors, hereby underscoring the robustness of HIV-1 RNA sensing mechanisms.
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Helga-Maria, C., Marie-Louise Hammarskjöld, and David Rekosh. "An Intact TAR Element and Cytoplasmic Localization Are Necessary for Efficient Packaging of Human Immunodeficiency Virus Type 1 Genomic RNA." Journal of Virology 73, no. 5 (1999): 4127–35. http://dx.doi.org/10.1128/jvi.73.5.4127-4135.1999.

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ABSTRACT Although most reports defining the human immunodeficiency virus type 1 (HIV-1) genomic RNA packaging signal have focused on the region downstream of the major 5′ splice site, others have suggested that sequences upstream of the splice site may also play an important role. In this study we have directly examined the role played by the HIV-1 TAR region in RNA packaging. For these experiments we used a proviral expression system that is largely independent of Tat for transcriptional activation. This allowed us to create constructs that efficiently expressed RNAs carrying mutations in TAR and to determine the ability of these RNAs to be packaged. Our results indicate that loss of sequences in TAR significantly reduce the ability of a viral RNA to be packaged. The requirement for TAR sequences in RNA packaging was further examined by using a series of missense mutations positioned throughout the entire TAR structure. TAR mutations previously shown to influence Tat transactivation, such as G31U in the upper loop region or UCU to AAG in the bulge (nucleotides [nt] 22 to 24), failed to have any effect on RNA packaging. Mutations which disrupted the portion of the TAR stem immediately below the bulge also had little effect. In contrast, dramatic effects on RNA packaging were observed with constructs containing mutations in the lower portion of the TAR stem. Point mutations which altered nt 5 to 9, 10 to 15, 44 to 49, or 50 to 54 all reduced RNA packaging 11- to 25-fold. However, compensatory double mutations which restored the stem structure were able to restore packaging. These results indicate that an intact lower stem structure, rather than a specific sequence, is required for RNA packaging. Our results also showed that RNA molecules retained within the nucleus cannot be packaged, unless they are transported to the cytoplasm by either Rev/Rev response element or the Mason-Pfizer monkey virus constitutive transport element.
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Chesnokov, Vladimir V., Pavel P. Dik, and Aleksandra S. Chichkan. "Formic Acid as a Hydrogen Donor for Catalytic Transformations of Tar." Energies 13, no. 17 (2020): 4515. http://dx.doi.org/10.3390/en13174515.

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Specific features of the catalytic tar cracking in the presence of formic acid, BEA zeolite and 8% Ni-2.5% Mo/Sibunit catalyst were studied at 350 °C and 1.0 MPa pressure. The obtained results evidenced that formic acid can be used as a hydrogen donor during catalytic reactions. The formic acid addition made it possible to perform efficient hydrocracking of heavy feed such as tar. It was found that both the tar conversion and selectivity to light (gasoline-diesel) fractions grew in the sequence: tar < (tar - formic acid) < (tar - formic acid - BEA zeolite) < (tar - formic acid - BEA zeolite - 8% Ni-2.5% Mo/Sibunit catalyst). Furthermore, significantly lower concentrations of impurities containing sulfur and nitrogen were observed for the (tar - formic acid - BEA zeolite - 8% Ni-2.5% Mo/Sibunit catalyst) system. For example, the sulfur and nitrogen concentrations in the tar precursor were 1.50% and 0.86%, respectively. Meanwhile, their concentrations in the liquid products after the catalytic cracking were 0.73% and 0.18%, respectively.
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Dissertations / Theses on the topic "Sequence tar"

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Ducongé, Frédéric. "Sélection in vitro d'aptamères ARN pouvant interagir avec la structure ARN TAR du VIH-1." Bordeaux 2, 1999. http://www.theses.fr/1999BOR28671.

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Esteves, Michelle Pereira. "Systematic analysis of expressed sequence tag (EST) databases to identify novel breast markers in breast cancer." Thesis, Royal Holloway, University of London, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537516.

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簡建顥 and Kin-ho Kan. "The effect of mental imagery in the performance and recall of a sequence of Tai Chi movements." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31257239.

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Kan, Kin-ho. "The effect of mental imagery in the performance and recall of a sequence of Tai Chi movements /." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23435884.

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BEZERRA, NETO João Pacífico. "Caracterização genética e análise evolutiva In silico de aquaporinas em feijão-caupi (Vigna unguiculata (L.) Walp.)." Universidade Federal de Pernambuco, 2012. https://repositorio.ufpe.br/handle/123456789/12301.

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CAPES; CNPQ; FACEPE; BNB; FINEP
O feijão-caupi é uma das mais antigas leguminosas cultivadas, com destacada importância em áreas tropicais e subtropicais. No Brasil, é uma das principais fontes de nutrientes para a dieta humana e animal, representando 80% da produção de grãos nas regiões norte e nordeste. Entretanto, fatores como seca e salinidade (as duas principais adversidades ambientais em regiões semiáridas) têm prejudicado tanto a quantidade quanto a qualidade da produção do feijão-caupi. Neste sentido, o estudo de proteínas que agem como facilitadoras da passagem de água entre as membranas biológicas e na prevenção da passagem de íons e outros solutos na célula é fundamental para o entendimento de como algumas plantas respondem a tais adversidades. Entre estas proteínas as aquaporinas merecem atenção, tratandose de uma família de pequenas proteínas transmembranas (24-30 kDa), dividida em quatro subfamílias, incluindo as Proteínas de Membrana Plasmática (PIP), Proteínas de Membrana de Tonoplasto (TIP), Proteínas de Membrana de Nódulos (NIP) e Pequenas Proteínas Básicas Intrínsecas de Membrana (SIP). Apesar da grande quantidade de dados sobre aquaporinas nos vegetais, nada se sabe sobre estes transportadores em algumas culturas de importância econômica, como o feijãocaupi. Utilizando dados de EST (Expressed Sequence Tags), 37 transcritos candidatos a aquaporinas foram identificados em feijão-caupi por meio de buscas com ferramentas de bioinformática, onde 27 apresentavam o domínio íntegro e 10 encontravam-se incompletas. Análises fenéticas das sequências de aminoácidos dividiram esta família nas quatro subfamílias já conhecidas para outras espécies vegetais, sendo 11 PIPs (cinco PIP1 e seis PIP2), 10 TIPs (quatro TIP3 e seis TIP), quatro NIPs e duas SIPs. Os alinhamentos múltiplos gerados a partir das sequências com domínio MIP completo, indicaram que as regiões ar/R das aquaporinas do feijão-caupi, em sua maioria, são similares às presentes em Arabidopsis, milho e arroz, apontando para afinidades com o mesmo tipo de soluto transportado. A expressão dos transcritos foi observada em todos os tecidos vegetais, estando associadas ao transporte de diferentes tipos de solutos nos compartimentos celulares. As aquaporinas identificadas neste estudo representam um importante recurso genético, fornecendo alvos em potencial para modificar as propriedades do uso de água em feijão-caupi ou em outras leguminosas relacionadas.
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Hultin, Emilie. "Genetic Sequence Analysis by Microarray Technology." Doctoral thesis, Stockholm : School of Biotechnology, Royal Institute of Technology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4330.

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Hijazi, Issa, and Pontus Pettersson. "Animal ID Tag Recognition with Convolutional and Recurrent Neural Network : Identifying digits from a number sequence with RCNN." Thesis, Högskolan i Skövde, Institutionen för informationsteknologi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-17031.

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Major advances in machine learning have made image recognition applications, with Artificial Neural Network, blossom over the recent years. The aim of this thesis was to find a solution to recognize digits from a number sequence on an ID tag, used to identify farm animals, with the help of image recognition. A Recurrent Convolutional Neural Network solution called PPNet was proposed and tested on a data set called Animal Identification Tags. A transfer learning method was also used to test if it could help PPNet generalize and better recognize digits. PPNet was then compared against Microsoft Azures own image recognition API, to determine how PPNet compares to a general solution. PPNet, while not performing as good, still managed to achieve competitive results to the Azure API.
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Alexsson, Andrei. "Unsupervised hidden Markov model for automatic analysis of expressed sequence tags." Thesis, Linköpings universitet, Bioinformatik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-69575.

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This thesis provides an in-depth analyze of expressed sequence tags (EST) that represent pieces of eukaryotic mRNA by using unsupervised hidden Markov model (HMM). ESTs are short nucleotide sequences that are used primarily for rapid identificationof new genes with potential coding regions (CDS). ESTs are made by sequencing on double-stranded cDNA and the synthesizedESTs are stored in digital form, usually in FASTA format. Since sequencing is often randomized and that parts of mRNA contain non-coding regions, some ESTs will not represent CDS.It is desired to remove these unwanted ESTs if the purpose is to identifygenes associated with CDS. Application of stochastic HMM allow identification of region contents in a EST. Softwares like ESTScanuse HMM in which a training of the HMM is done by supervised learning with annotated data. However, because there are not always annotated data at hand this thesis focus on the ability to train an HMM with unsupervised learning on data containing ESTs, both with and without CDS. But the data used for training is not annotated, i.e. the regions that an EST consists of are unknown. In this thesis a new HMM is introduced where the parameters of the HMM are in focus so that they are reasonablyconsistent with biologically important regionsof an mRNA such as the Kozak sequence, poly(A)-signals and poly(A)-tails to guide the training and decoding correctly with ESTs to proper statesin the HMM. Transition probabilities in the HMMhas been adapted so that it represents the mean length and distribution of the different regions in mRNA. Testing of the HMM's specificity and sensitivityhave been performed via BLAST by blasting each EST and compare the BLAST results with the HMM prediction results.A regression analysis test shows that the length of ESTs used when training the HMM is significantly important, the longer the better. The final resultsshows that it is possible to train an HMM with unsupervised machine learning but to be comparable to supervised machine learning as ESTScan, further expansion of the HMM is necessary such as frame-shift correction of ESTs byimproving the HMM's ability to choose correctly positioned start codons or nucleotides. Usually the false positive results are because of incorrectly positioned start codons leadingto too short CDS lengths. Since no frame-shift correction is implemented, short predicted CDS lengths are not acceptable and is hence not counted as coding regionsduring prediction. However, when there is a lack of supervised models then unsupervised HMM is a potential replacement with stable performance and able to be adapted forany eukaryotic organism.
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Silva, Marcicleide Lima da. "Estudo de genes expressos em frutos de camu-camu: seqüenciamento de ests." Universidade Federal do Amazonas, 2006. http://tede.ufam.edu.br/handle/tede/4385.

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CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
The camu-camu (Myrciaria dubia (H.B.K.) McVaugh) is a native sort of the Amazonian region, whose fruit presents elevated content of ascorbic acid (vitamin C). The study of the functional genome in camu-camu fruits has like base the expressed sequence tags sequencing - ESTs. Faced with the displayed the present thesis is going to analyze and identify express genes in camu-camu fruits by means of ESTs sequencing. The total RNA was extracted from the shell-pulp. The extremity 5’sequencing' of cDNA insert was carried out so much in the Technology of the DNA Laboratory (UFAM) and in the Sequencing Platform (EMBRAPA/CENARGEN). The ESTs sequences obtained were submitted to the System Genome, program of genomic annotation that integrates analysis management programs and viewing of nucleotides sequences. It developed an efficient procedure for total RNA extraction of camu-camu fruits that enabled the obtaining of mRNAs of quality, utilized in the making of cDNAs of sizes varied (500pb to 4Kb). From the sequencing were obtained 3196 ESTs valid, being formed 1546 singletons and 358 contigs, resulting of 2586 ESTs sequences in total with similarity the sequences found in the gene bank. The analysis library clusterization revealed an index of 81% novelty and 32,54% redundancy. Around 90% of the contigs presented decrease redundancy (2-4 reads by contigs). The facts of the categorization of the proteins identified detached the posttranslational modification, protein turnover, chaperones (13,2%) category. From the hoist of the species with bigger number of ESTs with similarity the camu-camu sequences detached itself Arabidopsis thaliana with 49%. Around 10 uniques presented very high similarity (and-value 0.0) to known genes. The ESTs more abundantly express in camu-camu fruits encode to gluthatione s-transferase. They were observed around 3% sequences (97 ESTs) with decrease similarity (e-value > e-10) and 15% did not they present similarity with no contained sequence in the gene bank. They were identified 138 ESTs sequences (4,3%) that they encode molecular chaperones with prevalence of the sHSP family that represents 33% of express chaperones. ESTs related to the ascorbic acid metabolism also were identified, being nine related the synthesis and six come back for ascorbic acid conversion and recycling. ESTs related to the ripening and mechanisms of defense of the fruit also were noticeable.
O camu-camu (Myrciaria dúbia (H.B.K.) McVaugh) é uma espécie nativa da região Amazônica, cujo fruto apresenta elevado teor de ácido ascórbico (vitamina C). O estudo do genoma funcional em frutos de camu-camu tem como base o seqüenciamento de fragmentos de seqüências expressas - ESTs (Expressed Sequence Tags). Diante do exposto a presente tese pretende analisar e identificar genes expressos em frutos de camu-camu por meio de seqüenciamento de ESTs. O RNA total foi extraído a partir da casca-polpa. O seqüenciamento da extremidade 5’ de insertos de cDNA foi realizado tanto no Laboratório de Tecnologia do DNA da UFAM e como na Plataforma de Seqüenciamento da EMBRAPA/CENARGEN. As seqüências ESTs obtidas foram submetidas ao Sistema Genoma, programa de anotação genômica que integra programas de gerenciamento de análise e visualização de seqüências nucleotídicas. Os resultados obtidos foram o desenvolvimento de um procedimento eficiente para extração de RNA total de frutos de camu-camu que possibilitou a obtenção de mRNAs de qualidade, utilizados na confecção de cDNAs de tamanhos variados (500pb a 4Kb). A partir do seqüenciamento foram obtidas 3196 ESTs válidas, sendo formados 1546 singletons e 358 contigs, resultando num total de 2586 seqüências ESTs com similaridade a seqüências encontradas no banco de genes. A análise da clusterização da biblioteca revelou um índice de 81% de novidade e 33% de redundância. Cerca de 90% dos contigs apresentaram baixa redundância (2-4 reads por contigs). Os dados da categorização das proteínas identificadas destacaram a categoria modificação pós-traducional, proteína turnover, chaperonas (13,2%). A partir do levantamento das espécies com maior número de ESTs com similaridade a seqüências de camu-camu destacou-se Arabidopsis thaliana com 49%. Cerca de 10 uniques apresentaram altíssima similaridade (e-value 0.0) a genes conhecidos. Os ESTs mais abundantemente expresso em frutos de camu-camu codificam a glutationa s-transferase. Foram observados cerca de 3% de seqüências (97 ESTs) com baixa similaridade (e-value > e-1010) e 15% não apresentaram similaridade com nenhuma seqüência contida no banco de genes. Foram identificadas 138 seqüências ESTs (4,3%) que codificam chaperonas moleculares com destaque à família sHSP que representa 33% das chaperonas expressas. ESTs relacionados ao metabolismo do ácido ascórbico também foram identificados, sendo nove relacionados a síntese e seis voltados para conversão e reciclagem do ácido ascórbico. ESTs relacionados ao amadurecimento e mecanismos de defesa do fruto também foram destacados.
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Khajuria, Chitvan. "Genomic, expression and functional analysis of genes from larval gut of the European corn borer, Ostrinia nubilalis (Hübner)." Diss., Kansas State University, 2010. http://hdl.handle.net/2097/2461.

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Doctor of Philosophy
Department of Entomology
Larry L. Buschman
Kun Yan Zhu
Genomic information for lepidopteran insects, particularly agricultural pest species, is very limited but urgently needed due to their economic importance and biodiversity. The huge economic losses ($ 1-2 billons / year) caused by the European corn borer (Ostrinia nubilalis, Hübner, ECB) makes this insect species one of the major pests of corn in the United States and western world. Management of ECB by conventional methods is limited but has had a great success by transgenic Bt (Bacillus thuringiensis) corn, which targets insect gut. However, the widespread use of Bt corn may lead to the development of Bt resistance in ECB. Knowledge of genes expressed in the insect gut is considered crucial for understanding basic physiology of food digestion, their interactions with Bt toxins and pathogens, and for discovering new targets for pest management. A large database of 15,000 expressed sequence tags (ESTs) was established from the ECB larval gut. To our knowledge, this database represents the largest gut-specific EST database from a lepidopteran pest. Analysis of 10 aminopeptidase-like genes between Cry1Ab–resistant and –susceptible ECB larvae revealed that aminopeptidase P-like (OnAPP) gene is a strong candidate for its role in Bt toxicity and resistance. The RNA interference mediated reduction in the transcript level of OnAPP gene in ECB larvae resulted in their reduced susceptibily to Cry1Ab. Analysis of the chitinase-like gene (OnCht) revealed its essential role in regulating chitin content of peritrophic membrane (PM). Our results suggest that OnCht may influence food digestion, nutrient absorption or movement of digestive enzymes through the PM and can be an important target for insect management. We also identified and characterized six genes involved in the innate immune defense response in ECB and showed that the expression of these genes were induced when challenged with bacteria. In addition to these results, this research generated significant genomic information for the development of microarray from the larval gut of ECB. The establishment of the feeding-based RNA interference technique could potentially help in delivering dsRNA orally to ECB for high throughput screening of effective genes to be targeted for insect pest management.
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Books on the topic "Sequence tar"

1

Kahl, Günter, and Matthias Harbers. Tag-based next generation sequencing. Wiley-Blackwell, 2012.

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1964-, Shao Longyi, ed. Lu xi nan shi tan xi - er die xi shen bu mei tan zi yuan fu cun gui lv yu zi yuan yu ce. Di zhi chu ban she, 2010.

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Ceng xu di ceng xue ji qi zai Talimu Pendi shi tan xi yan jiu zhong de ying yong. Shi you gong ye chu ban she, 1996.

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Cooper, Susan. Mahā songkhrām hǣng montrā tō̜n tai phūphā nư̄a mahā nathī =: Over sea, under stone : the dark is rising sequence. Enter Books, 2004.

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Harbers, Matthias, and Guenter Kahl. Tag-Based Next Generation Sequencing. Wiley & Sons, Incorporated, John, 2011.

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Sacadura, Nuno Tiago. Expressed sequence tag analyses of Ustilago maydis teliospore germination. 2004.

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Nugent, Kimberly G. Gene expression during Ustilago maydis diploid filamentous growth: Functional and comparative 'expressed sequence tag' analysis. 2003.

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Zola, Émile, and Patrick McGuinness. The Conquest of Plassans. Translated by Helen Constantine. Oxford University Press, 2014. http://dx.doi.org/10.1093/owc/9780199664788.001.0001.

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‘Abbé Faujas has arrived!’ The arrival of Abbé Faujas in the provincial town of Plassans has profound consequences for the community, and for the family of François Mouret in particular. Faujas and his mother come to lodge with François, his wife Marthe, and their three children, and Marthe quickly falls under the influence of the priest. Ambitious and unscrupulous, Faujas gradually infiltrates into all quarters of the town, intent on political as well as religious conquest. Intrigue, slander, and insinuation tear the townsfolk apart, creating suspicion and distrust, and driving the Mourets to ever more extreme actions. The fourth novel in Zola's Rougon-Macquart sequence, The Conquest of Plassans returns to the fictional Provençal town from which the family sprang in The Fortune of the Rougons. In one of the most psychological of his novels, Zola links small-town politics to the greater political and national dramas of the Second Empire.
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Wiener, Harvey S. Any Child Can Read Better. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195102185.001.0001.

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Reading, however fundamental the task may seem to everyday life, is a complex process that takes years to master. Yet, learning to read in the early stages is not an overwhelming problem for most children, especially when their classroom learning is coupled with a nurturing home environment in which reading is cherished, and pencil and paper are always available and fun to use. In fact, studies have shown that children score higher in reading if their parents support and encourage them at home. Unfortunately, though many parents want to involve themselves actively in their children's education, very few know just what to do. Now Dr. Harvey S. Wiener, author of the classic Any Child Can Write, provides an indispensable guide for parents who want to help their children enter the magic realm of words. In Any Child Can Read Better, Second Edition, Dr. Wiener offers practical advice on how to help children make their way through the maze of assignments and exercises related to classroom reading. In this essential book, parents learn how to be "reading helpers" without replacing or superseding the teacher--by supporting a child's reading habits and sharing the pleasures of fiction, poetry, and prose. Home learning parents also will find a wealth of information here. Through comfortable conversation and enjoyable exercises that tap children's native abilities, parents can help their child practice the critical thinking and reading skills that guarantee success in the classroom and beyond. For example, Dr. Wiener explains how exercises such as prereading warm-ups like creating word maps (a visual scheme that represents words and ideas as shapes and connects them) will allow youngsters to create a visual format and context before they begin reading. He shows how pictures from a birthday party can be used to create patterns of meaning by arranging them chronologically to allow the party's "story" to emerge, or how they might by arranged by order of importance--a picture of Beth standing at the door waiting for her friends to arrive could be displayed first, Beth blowing out the birthday cake placed toward the middle of the arrangement, and the pictures of Beth opening her gifts, especially the skates she's been begging for all year, would surely go toward the end of the sequence. Dr. Wiener shows how these activities, and many others, such as writing games, categorizing toys or clothes or favorite foods, and reading journals, will help children draw meaning out of written material. This second edition includes a new chapter describing the benefits of encouraging children to keep a journal of their personal reactions to books, the value of writing in the books they own (underlining, writing in the margins, and making a personal index) and a variety of reading activities to help children interact with writers and their books. Dr. Wiener has also expanded and updated his fascinating discussion of recommended books for children of all ages, complete with plot summaries. Written in simple, accessible prose, Any Child Can Read Better offers sensible advice for busy parents concerned with their children's education.
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Book chapters on the topic "Sequence tar"

1

Shi, Xuewen, Heyan Huang, Shuyang Zhao, Ping Jian, and Yi-Kun Tang. "Tag Recommendation by Word-Level Tag Sequence Modeling." In Database Systems for Advanced Applications. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-18590-9_58.

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Grote, Korbinian, and Thomas Werner. "Multidimensional Context of Sequence Tags: Biological Data Integration." In Tag-Based Next Generation Sequencing. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644582.ch26.

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Ruperao, Pradeep. "TAG Sequence Identification of Genomic Regions Using TAGdb." In Plant Bioinformatics. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3167-5_12.

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Pedretti, Kevin, Todd Scheetz, Terry Braun, Chad Roberts, Natalie Robinson, and Thomas Casavant. "A Parallel Expressed Sequence Tag (EST) Clustering Program." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/3-540-44743-1_51.

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Clifton, Sandra W., and Makedonka Mitreva. "Strategies for Undertaking Expressed Sequence Tag (EST) Projects." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-136-3_2.

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Frazier, Taylor P., and Baohong Zhang. "Identification of Plant microRNAs Using Expressed Sequence Tag Analysis." In Methods in Molecular Biology. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-682-5_2.

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Bercoff, Christiane. "A family of tag systems for paperfolding sequences." In STACS 95. Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/3-540-59042-0_82.

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Aoki, Takashi, Carl Tucker, and Ikuo Hirono. "Expressed sequence tag analyses of the Japanese flounder, Paralichthys olivaceus." In Aquatic Genomics. Springer Japan, 2003. http://dx.doi.org/10.1007/978-4-431-65938-9_9.

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Neote, Kuldeep S., and Shaun R. McColl. "Novel Chemokines Identified in Expressed Sequence Tag Databases via Bioinformatics." In Chemokines in Disease. Humana Press, 1999. http://dx.doi.org/10.1007/978-1-59259-706-2_2.

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Schmitt, Armin O. "Mining Expressed Sequence Tag (EST) Libraries for Cancer-Associated Genes." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-545-9_6.

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Conference papers on the topic "Sequence tar"

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Kuliński, Tadeusz, Łukasz Bielecki, Mikołaj Olejniczak, Izabela Zagorowska, and Ryszard W. Adamiak. "Structure and dynamics of the apical loop region of 29-mer hairpin of the TAR RNA HIV-1 sequence." In XIth Symposium on Chemistry of Nucleic Acid Components. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902191.

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2

Coria, Ibai, Mikel Abasolo, Josu Aguirrebeitia, and Iker Heras. "VBA APP for the Calculation of Optimal Tightening Sequences for Ring Type Joints." In ASME 2017 Pressure Vessels and Piping Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/pvp2017-66252.

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For pressure vessels gasketed joints, obtaining a uniform bolt load distribution is mandatory in order to ensure leak-free service of the joint. However, due to the elastic interaction phenomenon, it is difficult to achieve a uniform bolt load distribution. To address this difficulty, standards recommend tightening sequences that have shown good performance. However, these sequences have to be carried out in several passes; in addition, the standards point out that each assembler should develop its particular tightening sequences. In order to overcome these disadvantages, it is possible to find methods that provide a particular tightening sequence with which a uniform bolt load is obtained in a single pass tightening sequence. The most popular method is the Elastic Interaction Coefficients Method (EICM). In previous works [1,2], a new methodology called Tetraparametric Assembly Method (TAM) was developed for ASME Ring Type Joints (RTJ). In comparison with the EICM, the TAM provides very accurate results with much lower cost. In this work, the TAM has been implemented in Microsoft Excel (programmed in Visual Basic for Application), to obtain in a few seconds an optimal tightening sequence for most RTJ (NPS, Class and SCHD) for any target load and any assembly pattern using one or two passes.
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3

Wang, Jiapeng, Tianwei Wang, Guozhi Tang, et al. "Tag, Copy or Predict: A Unified Weakly-Supervised Learning Framework for Visual Information Extraction using Sequences." In Thirtieth International Joint Conference on Artificial Intelligence {IJCAI-21}. International Joint Conferences on Artificial Intelligence Organization, 2021. http://dx.doi.org/10.24963/ijcai.2021/150.

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Visual information extraction (VIE) has attracted increasing attention in recent years. The existing methods usually first organized optical character recognition (OCR) results in plain texts and then utilized token-level category annotations as supervision to train a sequence tagging model. However, it expends great annotation costs and may be exposed to label confusion, the OCR errors will also significantly affect the final performance. In this paper, we propose a unified weakly-supervised learning framework called TCPNet (Tag, Copy or Predict Network), which introduces 1) an efficient encoder to simultaneously model the semantic and layout information in 2D OCR results, 2) a weakly-supervised training method that utilizes only sequence-level supervision; and 3) a flexible and switchable decoder which contains two inference modes: one (Copy or Predict Mode) is to output key information sequences of different categories by copying a token from the input or predicting one in each time step, and the other (Tag Mode) is to directly tag the input sequence in a single forward pass. Our method shows new state-of-the-art performance on several public benchmarks, which fully proves its effectiveness.
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Wu, Chao. "Visualization of Tag Sequence." In 2008 International Conference on Computer Science and Software Engineering (CSSE 2008). IEEE, 2008. http://dx.doi.org/10.1109/csse.2008.333.

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Zhang, Yuan, Hongshen Chen, Yihong Zhao, Qun Liu, and Dawei Yin. "Learning Tag Dependencies for Sequence Tagging." In Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/637.

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Sequence tagging is the basis for multiple applications in natural language processing. Despite successes in learning long term token sequence dependencies with neural network, tag dependencies are rarely considered previously. Sequence tagging actually possesses complex dependencies and interactions among the input tokens and the output tags. We propose a novel multi-channel model, which handles different ranges of token-tag dependencies and their interactions simultaneously. A tag LSTM is augmented to manage the output tag dependencies and word-tag interactions, while three mechanisms are presented to efficiently incorporate token context representation and tag dependency. Extensive experiments on part-of-speech tagging and named entity recognition tasks show that the proposed model outperforms the BiLSTM-CRF baseline by effectively incorporating the tag dependency feature.
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Xie, Chunyu, Ce Li, Baochang Zhang, Chen Chen, Jungong Han, and Jianzhuang Liu. "Memory Attention Networks for Skeleton-based Action Recognition." In Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/227.

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Skeleton-based action recognition task is entangled with complex spatio-temporal variations of skeleton joints, and remains challenging for Recurrent Neural Networks (RNNs). In this work, we propose a temporal-then-spatial recalibration scheme to alleviate such complex variations, resulting in an end-to-end Memory Attention Networks (MANs) which consist of a Temporal Attention Recalibration Module (TARM) and a Spatio-Temporal Convolution Module (STCM). Specifically, the TARM is deployed in a residual learning module that employs a novel attention learning network to recalibrate the temporal attention of frames in a skeleton sequence. The STCM treats the attention calibrated skeleton joint sequences as images and leverages the Convolution Neural Networks (CNNs) to further model the spatial and temporal information of skeleton data. These two modules (TARM and STCM) seamlessly form a single network architecture that can be trained in an end-to-end fashion. MANs significantly boost the performance of skeleton-based action recognition and achieve the best results on four challenging benchmark datasets: NTU RGB+D, HDM05, SYSU-3D and UT-Kinect.
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Kun, Andrew L., Travis Royer, and Adam Leone. "Using tap sequences to authenticate drivers." In the 5th International Conference. ACM Press, 2013. http://dx.doi.org/10.1145/2516540.2516567.

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Dan, Haitao, Robert M. Hierons, and Steve Counsell. "A Thread-tag Based Semantics for Sequence Diagrams." In Fifth IEEE International Conference on Software Engineering and Formal Methods (SEFM 2007). IEEE, 2007. http://dx.doi.org/10.1109/sefm.2007.3.

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Zhong, Yujie, and Liutong Xu. "TagNet: Tag Out the Value Sequence of SQL Statement." In 2019 International Conference on Intelligent Computing, Automation and Systems (ICICAS). IEEE, 2019. http://dx.doi.org/10.1109/icicas48597.2019.00173.

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Li, Hui, Chunmei Liu, Xumin Liu, et al. "Peptide Sequence Tag-Based Blind Identification-based SVM Model." In 2010 International Conference on Machine Learning and Applications (ICMLA). IEEE, 2010. http://dx.doi.org/10.1109/icmla.2010.156.

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Reports on the topic "Sequence tar"

1

Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using Tau RNA Sequences. Defense Technical Information Center, 1991. http://dx.doi.org/10.21236/ada254451.

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