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Artykuły w czasopismach na temat "Sequence Feature"
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Liu, Zhi-Hua, Dian Jiao i Xiao Sun. "Classifying Genomic Sequences by Sequence Feature Analysis". Genomics, Proteomics & Bioinformatics 3, nr 4 (2005): 201–5. http://dx.doi.org/10.1016/s1672-0229(05)03027-5.
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Caspi, Yaron, Denis Simakov i Michal Irani. "Feature-Based Sequence-to-Sequence Matching". International Journal of Computer Vision 68, nr 1 (1.03.2006): 53–64. http://dx.doi.org/10.1007/s11263-005-4842-z.
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Zhang, Tianjiao, Rongjie Wang, Qinghua Jiang i Yadong Wang. "An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers". Current Bioinformatics 15, nr 6 (11.11.2020): 574–80. http://dx.doi.org/10.2174/1574893614666191120141032.
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Background: Enhancers are cis-regulatory elements that enhance gene expression on DNA sequences. Since most of enhancers are located far from transcription start sites, it is difficult to identify them. As other regulatory elements, the regions around enhancers contain a variety of features, which can help in enhancer recognition. Objective: The classification power of features differs significantly, the performances of existing methods that use one or a few features for identifying enhancer vary greatly. Therefore, evaluating the classification power of each feature can improve the predictive performance of enhancers. Methods: We present an evaluation method based on Information Gain (IG) that captures the entropy change of enhancer recognition according to features. To validate the performance of our method, experiments using the Single Feature Prediction Accuracy (SFPA) were conducted on each feature. Results: The average IG values of the sequence feature, transcriptional feature and epigenetic feature are 0.068, 0.213, and 0.299, respectively. Through SFPA, the average AUC values of the sequence feature, transcriptional feature and epigenetic feature are 0.534, 0.605, and 0.647, respectively. The verification results are consistent with our evaluation results. Conclusion: This IG-based method can effectively evaluate the classification power of features for identifying enhancers. Compared with sequence features, epigenetic features are more effective for recognizing enhancers.
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SHAN, YING, HARPREET S. SAWHNEY i ART POPE. "CLUSTERING MULTIPLE IMAGE SEQUENCES WITH A SEQUENCE-TO-SEQUENCE SIMILARITY MEASURE". International Journal of Pattern Recognition and Artificial Intelligence 19, nr 04 (czerwiec 2005): 551–64. http://dx.doi.org/10.1142/s0218001405004149.
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We propose a novel similarity measure of two image sequences based on shapeme histograms. The idea of shapeme histogram has been used for single image/texture recognition, but is used here to solve the sequence-to-sequence matching problem. We develop techniques to represent each sequence as a set of shapeme histograms, which captures different variations of the object appearances within the sequence. These shapeme histograms are computed from the set of 2D invariant features that are stable across multiple images in the sequence, and therefore minimizes the effect of both background clutter, and 2D pose variations. We define sequence similarity measure as the similarity of the most similar pair of images from both sequences. This definition maximizes the chance of matching between two sequences of the same object, because it requires only part of the sequences being similar. We also introduce a weighting scheme to conduct an implicit feature selection process during the matching of two shapeme histograms. Experiments on clustering image sequences of tracked objects demonstrate the efficacy of the proposed method.
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Pugin, E. V., i A. L. Zhiznyakov. "CLASSIFICATION OF FEATURES OF IMAGE SEQUENCES". ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XL-5/W6 (18.05.2015): 79–81. http://dx.doi.org/10.5194/isprsarchives-xl-5-w6-79-2015.
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Processing of image sequences is a very actual trend now. This is confirmed with a vast amount of researches in that area. The possibility of an image sequence processing and pattern recognition became available because of increased computer capabilities and better photo and video cameras. The feature extraction is one of the main steps during image processing and pattern recognition. This paper presents a novel classification of features of image sequences. The proposed classification has three groups: 1) features of a single image, 2) features of an image sequence, 3) semantic features of an observed scene. The first group includes features extracted from a single image. The second group consists of features of any kinds of image sequences. The third group contains semantic features. Reverse feature clarification method is the iterative method when on each iteration we use higher level features to extract lower level features more precisely. The proposed classification of features of image sequences solves a problem of decomposition of the source feature space into several groups. Reverse feature clarification method allows to increase the quality of image processing during iterative process.
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Vezzi, Francesco, Giuseppe Narzisi i Bud Mishra. "Feature-by-Feature – Evaluating De Novo Sequence Assembly". PLoS ONE 7, nr 2 (3.02.2012): e31002. http://dx.doi.org/10.1371/journal.pone.0031002.
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Tian, Huixin, i Qiangqiang Xu. "Time Series Prediction Method Based on E-CRBM". Electronics 10, nr 4 (8.02.2021): 416. http://dx.doi.org/10.3390/electronics10040416.
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To solve the problems of delayed prediction results and large prediction errors in one-dimensional time series prediction, a time series prediction method based on Error-Continuous Restricted Boltzmann Machines (E-CRBM) is proposed in this paper. This method constructs a deep conversion prediction framework, which is composed of two E-CRBMs and a neural network (NN). Firstly, the E-CRBM models of the original input sequence and the target prediction sequence are trained, respectively, to extract the time features of the two sequences. Then the NN model is used to connect and transform the time features. Secondly, the feature sequence H1 is extracted from the original input sequence of test data through E-CRBM1, which is used as input of NN to obtain feature transformation sequence H2. Finally, the target prediction sequence is obtained by reverse reconstruction of feature transformation sequence H2 through E-CRBM2. The E-CRBM in this paper introduces the residual sequence of NN feature transformation in the hidden layer of CRBM, which increases the robustness of CRBM and improves the overall prediction accuracy. The classical time series data (sunspot time series) and the actual operation data of reciprocating compressor are selected in the experiment. Compared with the traditional time series prediction method, the results verify the effectiveness of the proposed method in single-step prediction and multi-step prediction.
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AL-SHAHIB, ALI, RAINER BREITLING i DAVID GILBERT. "FRANKSUM: NEW FEATURE SELECTION METHOD FOR PROTEIN FUNCTION PREDICTION". International Journal of Neural Systems 15, nr 04 (sierpień 2005): 259–75. http://dx.doi.org/10.1142/s0129065705000281.
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In the study of in silico functional genomics, improving the performance of protein function prediction is the ultimate goal for identifying proteins associated with defined cellular functions. The classical prediction approach is to employ pairwise sequence alignments. However this method often faces difficulties when no statistically significant homologous sequences are identified. An alternative way is to predict protein function from sequence-derived features using machine learning. In this case the choice of possible features which can be derived from the sequence is of vital importance to ensure adequate discrimination to predict function. In this paper we have successfully selected biologically significant features for protein function prediction. This was performed using a new feature selection method (FrankSum) that avoids data distribution assumptions, uses a data independent measurement (p-value) within the feature, identifies redundancy between features and uses an appropiate ranking criterion for feature selection. We have shown that classifiers generated from features selected by FrankSum outperforms classifiers generated from full feature sets, randomly selected features and features selected from the Wrapper method. We have also shown the features are concordant across all species and top ranking features are biologically informative. We conclude that feature selection is vital for successful protein function prediction and FrankSum is one of the feature selection methods that can be applied successfully to such a domain.
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Et. al., Muthulakshmi M,. "A Novel Feature Extraction from Genome Sequences For Taxonomic Classification Of Living Organisms". Turkish Journal of Computer and Mathematics Education (TURCOMAT) 12, nr 2 (11.04.2021): 1436–51. http://dx.doi.org/10.17762/turcomat.v12i2.1364.
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Genome sequencing aids in understanding the nature, characteristics, habitat and evolutionary history of all living organisms. Apart from sequencing, the more important task is to correctly place the sequenced genome in the taxonomy. Generally, the taxonomic classification of the living organisms is done by observing their morphological, behavioral, genetic and biochemical characteristics. Among them, taxonomic classification using genetic observation is more accurate scientifically as the Genome sequence analysis exploits the complete characteristics of the organism. In this paper, we developed a novel Frequency based Feature Extraction Technique (FFET) which extracts 120 features and helps to analyze the genome sequence of the organism and to classify them in the taxonomy accordingly. We performed a kingdom level taxonomic classification using the proposed FFET. The proposed FFET extracts features based on storage, frequency of nucleotide bases, pattern arrangement and amino acid composition of genome sequences. The feature extraction technique is applied to 150 samples of genome sequences of various organisms which were downloaded from National Centre for Biotechnology and Information (NCBI) database. The extracted features are classified using various Machine learning and Deep learning classifiers. From the results, it is evident that FFET performs well for classification with Convolutional Neural Network (CNN) classifier with an accuracy of 96.73 %.
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Huang, Wen-Lin, Chun-Wei Tung, Chyn Liaw, Hui-Ling Huang i Shinn-Ying Ho. "Rule-Based Knowledge Acquisition Method for Promoter Prediction in Human andDrosophilaSpecies". Scientific World Journal 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/327306.
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The rapid and reliable identification of promoter regions is important when the number of genomes to be sequenced is increasing very speedily. Various methods have been developed but few methods investigate the effectiveness of sequence-based features in promoter prediction. This study proposes a knowledge acquisition method (named PromHD) based on if-then rules for promoter prediction in human andDrosophilaspecies. PromHD utilizes an effective feature-mining algorithm and a reference feature set of 167 DNA sequence descriptors (DNASDs), comprising three descriptors of physicochemical properties (absorption maxima, molecular weight, and molar absorption coefficient), 128 top-ranked descriptors of 4-mer motifs, and 36 global sequence descriptors. PromHD identifies two feature subsets with 99 and 74 DNASDs and yields test accuracies of 96.4% and 97.5% in human andDrosophilaspecies, respectively. Based on the 99- and 74-dimensional feature vectors, PromHD generates several if-then rules by using the decision tree mechanism for promoter prediction. The top-ranked informative rules with high certainty grades reveal that the global sequence descriptor, the length of nucleotide A at the first position of the sequence, and two physicochemical properties, absorption maxima and molecular weight, are effective in distinguishing promoters from non-promoters in human andDrosophilaspecies, respectively.
Rozprawy doktorskie na temat "Sequence Feature"
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Smith, Stephen Mark. "Feature based image sequence understanding". Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316951.
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Sung, Raymond Chun Wai. "Automatic assembly feature recognition and disassembly sequence generation". Thesis, Heriot-Watt University, 2001. http://hdl.handle.net/10399/478.
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Lai, Man Lok Michael. "Image sequence coding using intensity-based feature separation". Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284145.
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Tangirala, Karthik. "Unsupervised feature construction approaches for biological sequence classification". Diss., Kansas State University, 2015. http://hdl.handle.net/2097/19123.
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Doctor of PhilosophyDepartment of Computing and Information Sciences
Doina Caragea
Recent advancements in biological sciences have resulted in the availability of large amounts of sequence data (DNA and protein sequences). Biological sequence data can be annotated using machine learning techniques, but most learning algorithms require data to be represented by a vector of features. In the absence of biologically informative features, k-mers generated using a sliding window-based approach are commonly used to represent biological sequences. A larger k value typically results in better features; however, the number of k-mer features is exponential in k, and many k-mers are not informative. Feature selection is widely used to reduce the dimensionality of the input feature space. Most feature selection techniques use feature-class dependency scores to rank the features. However, when the amount of available labeled data is small, feature selection techniques may not accurately capture feature-class dependency scores. Therefore, instead of working with all k-mers, this dissertation proposes the construction of a reduced set of informative k-mers that can be used to represent biological sequences. This work resulted in three novel unsupervised approaches to construct features: 1. Burrows Wheeler Transform-based approach, that uses the sorted permutations of a given sequence to construct sequential features (subsequences) that occur multiple times in a given sequence. 2. Community detection-based approach, that uses a community detection algorithm to group similar subsequences into communities and refines the communities to form motifs (group of similar subsequences). Motifs obtained using the community detection-based approach satisfy the ZOMOPS constraint (Zero, One or Multiple Occurrences of a Motif Per Sequence). All possible unique subsequences of the obtained motifs are then used as features to represent the sequences. 3. Hybrid-based approach, that combines the Burrows Wheeler Transform-based approach and the community detection-based approach to allow certain mismatches to the features constructed using the Burrows Wheeler Transform-based approach. To evaluate the predictive power of the features constructed using the proposed approaches, experiments were conducted in three learning scenarios: supervised, semi-supervised, and domain adaptation for both nucleotide and protein sequence classification problems. The performance of classifiers learned using features generated with the proposed approaches was compared with the performance of the classifiers learned using k-mers (with feature selection) and feature hashing (another unsupervised dimensionality reduction technique). Experimental results from the three learning scenarios showed that features constructed with the proposed approaches were typically more informative than k-mers and feature hashing.
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Nilsson, Daniel. "Genomic feature identification in trypanosomatid parasites /". Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-789-8/.
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Bozkurt, Burcin. "Prediction Of Protein Subcellular Localization Using Global Protein Sequence Feature". Master's thesis, METU, 2003. http://etd.lib.metu.edu.tr/upload/3/1135292/index.pdf.
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The problem of identifying genes in eukaryotic genomic sequences by computational methods has attracted considerable research attention in recent years.
Many early approaches to the problem focused on prediction of individual functional elements and compositional properties of coding and non coding deoxyribonucleic acid (DNA) in entire eukaryotic gene structures. More recently, a number of approaches has been developed which integrate multiple types of information including structure, function and genetic properties of proteins. Knowledge of the structure of a protein is essential for describing and understanding its function. In addition, subcellular localization of a protein can be used to provide some amount of characterization of a protein. In this study, a method for the prediction of protein subcellular localization based on primary sequence data is described. Primary sequence data for a protein is based on amino acid sequence. The frequency value for each amino acid is computed in one given position. Assigned frequencies are used in a new encoding scheme that conserves biological information based on point accepted mutations (PAM) substitution matrix. This method can be used to predict the nuclear, the cytosolic sequences, the mitochondrial targeting peptides (mTP) and the signal peptides (SP). For clustering purposes, other than well known traditional techniques, principle component analysis (PCA)"and self-organizing maps (SOM)"
are used. For classication purposes, support vector machines (SVM)"
, a method of statistical learning theory recently introduced to bioinformatics is used. The aim of the combination of feature extraction, clustering and classification methods is to design an acccurate system that predicts the subcellular localization of proteins presented into the system. Our scheme for combining several methods is cascading or serial combination according to its architecture. In the cascading architecture, the output of a method serves as the input of the other model used.
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Islamaj, Rezarta. "Feature generation and analysis applied to sequence classification for splice-site prediction". College Park, Md.: University of Maryland, 2007. http://hdl.handle.net/1903/7745.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2007.Thesis research directed by: Dept. of Computer Science. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Lakshmanan, Arun. "Practice makes imperfect? sequence learning and the discontinuous acquisition of feature use skills /". [Bloomington, Ind.] : Indiana University, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3331241.
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Thesis (Ph.D.)--Indiana University, Kelley School of Business, 2008.Title from PDF t.p. (viewed on Jul 23, 2009). Source: Dissertation Abstracts International, Volume: 69-11, Section: A, page: 4418. Adviser: Shanker Krishnan.
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Ali, Isse. "Analysing and predicting differences between methylated and unmethylated DNA sequence features". Thesis, De Montfort University, 2015. http://hdl.handle.net/2086/12616.
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DNA methylation is involved in various biological phenomena, and its dysregulation has been demonstrated as being correlated with a number of human disease processes, including cancers, autism, and autoimmune, mental health and neuro-degenerative ones. It has become important and useful in characterising and modelling these biological phenomena in or-der to understand the mechanism of such occurrences, in relation to both health and disease. An attempt has previously been made to map DNA methylation across human tissues, however, the means of distinguishing between methylated, unmethylated and differentially-methylated groups using DNA sequence features remains unclear. The aim of this study is therefore to: firstly, investigate DNA methylation classes and predict these based on DNA sequence features; secondly, to further identify methylation-associated DNA sequence features, and distinguish methylation differences between males and females in relation to both healthy and diseased, sta-tuses. This research is conducted in relation to three samples within nine biological feature sub-sets extracted from DNA sequence patterns (Human genome database). Two samples contain classes (methylated, unmethy-lated and differentially-methylated) within a total of 642 samples with 3,809 attributes driven from four human chromosomes, i.e. chromosomes 6, 20, 21 and 22, and the third sample contains all human chromosomes, which encompasses 1628 individuals, and then 1,505 CpG loci (features) were extracted by using Hierarchical clustering (a process Heatmap), along with pair correlation distance and then applied feature selection methods. From this analysis, author extract 47 features associated with gender and age, with 17 revealing significant methylation differences between males and females. Methylation classes prediction were applied a K-nearest Neighbour classifier, combined with a ten-fold cross- validation, since to some data were severely imbalanced (i.e., existed in sub-classes), and it has been established that direct analysis in machine-learning is biased towards the majority class. Hence, author propose a Modified- Leave-One-Out (MLOO) cross-validation and AdaBoost methods to tackle these issues, with the aim of compositing a balanced outcome and limiting the bias in-terference from inter-differences of the classes involved, which has provided potential predictive accuracies between 75% and 100%, based on the DNA sequence context.
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Abril, Ferrando Josep Francesc. "Comparative analysis of eukaryotic gene sequence features". Doctoral thesis, Universitat Pompeu Fabra, 2005. http://hdl.handle.net/10803/7108.
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L'incessant augment del nombre de seqüències genòmiques, juntament amb l'increment del nombre de tècniques experimentals de les que es disposa,
permetrà obtenir el catàleg complet de les funcions cel.lulars de
diferents organismes, incloent-hi la nostra espècie. Aquest catàleg
definirà els fonaments sobre els que es podrà entendre millor com els
organismes funcionen a nivell molecular. Al mateix temps es tindran més
pistes sobre els canvis que estan associats amb les malalties. Per tant,
la seqüència en brut, tal i com s'obté dels projectes de seqüenciació de
genomes, no té cap valor sense les anàlisis i la subsegüent anotació de
les característiques que defineixen aquestes funcions. Aquesta tesi
presenta la nostra contribució en tres aspectes relacionats de
l'anotació dels gens en genomes eucariotes.
Primer, la comparació a nivell de seqüència entre els genomes humà i de
ratolí es va dur a terme mitjançant un protocol semi-automàtic. El
programa de predicció de gens SGP2 es va desenvolupar a partir
d'elements d'aquest protocol. El concepte al darrera de l'SGP2 és que
les regions de similaritat obtingudes amb el programa TBLASTX, es fan
servir per augmentar la puntuació dels exons predits pel programa
geneid, amb el que s obtenen conjunts d'anotacions més acurats
d'estructures gèniques. SGP2 té una especificitat que és prou gran com
per que es puguin validar experimentalment via RT-PCR. La validació de
llocs d'splicing emprant la tècnica de la RT-PCR és un bon exemple de
com la combinació d'aproximacions computacionals i experimentals
produeix millors resultats que per separat.
S'ha dut a terme l'anàlisi descriptiva a nivell de seqüència dels llocs
d'splicing obtinguts sobre un conjunt fiable de gens ortòlegs per humà,
ratolí, rata i pollastre. S'han explorat les diferències a nivell de
nucleòtid entre llocs U2 i U12, pel conjunt d'introns ortòlegs que se'n
deriva d'aquests gens. S'ha trobat que els senyals d'splicing ortòlegs
entre humà i rossegadors, així com entre rossegadors, estan més
conservats que els llocs no relacionats. Aquesta conservació addicional
pot ser explicada però a nivell de conservació basal dels introns.
D'altra banda, s'ha detectat més conservació de l'esperada entre llocs
d'splicing ortòlegs entre mamífers i pollastre. Els resultats obtinguts
també indiquen que les classes intròniques U2 i U12 han evolucionat
independentment des de l'ancestre comú dels mamífers i les aus. Tampoc
s'ha trobat cap cas convincent d'interconversió entre aquestes dues
classes en el conjunt d'introns ortòlegs generat, ni cap cas de
substitució entre els subtipus AT-AC i GT-AG d'introns U12. Al contrari,
el pas de GT-AG a GC-AG, i viceversa, en introns U2 no sembla ser inusual.
Finalment, s'han implementat una sèrie d'eines de visualització per
integrar anotacions obtingudes pels programes de predicció de gens i per
les anàlisis comparatives sobre genomes. Una d'aquestes eines, el
gff2ps, s'ha emprat en la cartografia dels genomes humà, de la mosca del
vinagre i del mosquit de la malària, entre d'altres. El programa
gff2aplot i els filtres associats, han facilitat la tasca d'integrar
anotacions de seqüència amb els resultats d'eines per la cerca
d'homologia, com ara el BLAST. S'ha adaptat també el concepte de
pictograma a l'anàlisi comparativa de llocs d splicing ortòlegs, amb el
desenvolupament del programa compi.
El aumento incesante del número de secuencias genómicas, junto con el
incremento del número de técnicas experimentales de las que se dispone,
permitirá la obtención del catálogo completo de las funciones celulares
de los diferentes organismos, incluida nuestra especie. Este catálogo
definirá las bases sobre las que se pueda entender mejor el
funcionamiento de los organismos a nivel molecular. Al mismo tiempo, se
obtendrán más pistas sobre los cambios asociados a enfermedades. Por
tanto, la secuencia en bruto, tal y como se obtiene en los proyectos de
secuenciación masiva, no tiene ningún valor sin los análisis y la
posterior anotación de las características que definen estas funciones.
Esta tesis presenta nuestra contribución a tres aspectos relacionados de
la anotación de los genes en genomas eucariotas.
Primero, la comparación a nivel de secuencia entre el genoma humano y el
de ratón se llevó a cabo mediante un protocolo semi-automático. El
programa de predicción de genes SGP2 se desarrolló a partir de elementos
de dicho protocolo. El concepto sobre el que se fundamenta el SGP2 es
que las regiones de similaridad obtenidas con el programa TBLASTX, se
utilizan para aumentar la puntuación de los exones predichos por el
programa geneid, con lo que se obtienen conjuntos más precisos de
anotaciones de estructuras génicas. SGP2 tiene una especificidad
suficiente como para validar esas anotaciones experimentalmente vía
RT-PCR. La validación de los sitios de splicing mediante el uso de la
técnica de la RT-PCR es un buen ejemplo de cómo la combinación de
aproximaciones computacionales y experimentales produce mejores
resultados que por separado.
Se ha llevado a cabo el análisis descriptivo a nivel de secuencia de los
sitios de splicing obtenidos sobre un conjunto fiable de genes ortólogos
para humano, ratón, rata y pollo. Se han explorado las diferencias a
nivel de nucleótido entre sitios U2 y U12 para el conjunto de intrones
ortólogos derivado de esos genes. Se ha visto que las señales de
splicing ortólogas entre humanos y roedores, así como entre roedores,
están más conservadas que las no ortólogas. Esta conservación puede ser
explicada en parte a nivel de conservación basal de los intrones. Por
otro lado, se ha detectado mayor conservación de la esperada entre
sitios de splicing ortólogos entre mamíferos y pollo. Los resultados
obtenidos indican también que las clases intrónicas U2 y U12 han
evolucionado independientemente desde el ancestro común de mamíferos y
aves. Tampoco se ha hallado ningún caso convincente de interconversión
entre estas dos clases en el conjunto de intrones ortólogos generado, ni
ningún caso de substitución entre los subtipos AT-AC y GT-AG en intrones
U12. Por el contrario, el paso de GT-AG a GC-AG, y viceversa, en
intrones U2 no parece ser inusual.
Finalmente, se han implementado una serie de herramientas de
visualización para integrar anotaciones obtenidas por los programas de
predicción de genes y por los análisis comparativos sobre genomas. Una
de estas herramientas, gff2ps, se ha utilizado para cartografiar los
genomas humano, de la mosca del vinagre y del mosquito de la malaria. El
programa gff2aplot y los filtros asociados, han facilitado la tarea de
integrar anotaciones a nivel de secuencia con los resultados obtenidos
por herramientas de búsqueda de homología, como BLAST. Se ha adaptado
también el concepto de pictograma al análisis comparativo de los sitios
de splicing ortólogos, con el desarrollo del programa compi.
The constantly increasing amount of available genome sequences, along
with an increasing number of experimental techniques, will help to
produce the complete catalog of cellular functions for different
organisms, including humans. Such a catalog will define the base from
which we will better understand how organisms work at the molecular
level. At the same time it will shed light on which changes are
associated with disease. Therefore, the raw sequence from genome
sequencing projects is worthless without the complete analysis and
further annotation of the genomic features that define those functions.
This dissertation presents our contribution to three related aspects of
gene annotation on eukaryotic genomes.
First, a comparison at sequence level of human and mouse genomes was
performed by developing a semi-automatic analysis pipeline. The SGP2
gene-finding tool was developed from procedures used in this pipeline.
The concept behind SGP2 is that similarity regions obtained by TBLASTX
are used to increase the score of exons predicted by geneid, in order to
produce a more accurate set of gene structures. SGP2 provides a
specificity that is high enough for its predictions to be experimentally
verified by RT-PCR. The RT-PCR validation of predicted splice junctions
also serves as example of how combined computational and experimental
approaches will yield the best results.
Then, we performed a descriptive analysis at sequence level of the
splice site signals from a reliable set of orthologous genes for human,
mouse, rat and chicken. We have explored the differences at nucleotide
sequence level between U2 and U12 for the set of orthologous introns
derived from those genes. We found that orthologous splice signals
between human and rodents and within rodents are more conserved than
unrelated splice sites. However, additional conservation can be
explained mostly by background intron conservation. Additional
conservation over background is detectable in orthologous mammalian and
chicken splice sites. Our results also indicate that the U2 and U12
intron classes have evolved independently since the split of mammals and
birds. We found neither convincing case of interconversion between these
two classes in our sets of orthologous introns, nor any single case of
switching between AT-AC and GT-AG subtypes within U12 introns. In
contrast, switching between GT-AG and GC-AG U2 subtypes does not appear
to be unusual.
Finally, we implemented visualization tools to integrate annotation
features for gene- finding and comparative analyses. One of those tools,
gff2ps, was used to draw the whole genome maps for human, fruitfly and
mosquito. gff2aplot and the accompanying parsers facilitate the task of
integrating sequence annotations with the output of homologybased tools,
like BLAST.We have also adapted the concept of pictograms to the
comparative analysis of orthologous splice sites, by developing compi.
Książki na temat "Sequence Feature"
1
Maroni, Gustavo. An atlas of Drosophila genes: Sequences and molecular features. New York: Oxford University Press, 1993.
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2
What's a sequencer?: A basic guide to their features and use. Milwaukee, WI, U.S.A: H. Leonard Pub. Corp., 1990.
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Emile, Menasché, red. What's a sequencer?: A basic guide to their features and use. Wyd. 2. Milwaukee: Hal Leonard, 2001.
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4
Neelanarayanan, red. Feature Analysis for Abnormality Detection in Breast Thermogram Sequences Subject to Cold Stress. VIT University Chennai, India: Association of Scientists, Developers and Faculties, 2014.
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5
Webb, Graham. The animated film encyclopedia: A complete guide to American shorts, features and sequences 1900-1979. Jefferson, N.C: McFarland, 2000.
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Webb, Graham. The animated film encyclopedia: A complete guide to American shorts, features, and sequences, 1900-1979. Jefferson, N.C: McFarland & Co., 2000.
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The animated film encyclopedia: A complete guide to American shorts, features, and sequences, 1900-1979. Jefferson, N.C: McFarland & Co., 2006.
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The animated film encyclopedia: A complete guide to American shorts, features and sequences, 1900-1999. Wyd. 2. Jefferson, N.C: McFarland & Co., 2011.
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Scherbak, Aleksey, Vladimir Andreev i Afanasiy Zubov. IT risk management. ru: INFRA-M Academic Publishing LLC., 2023. http://dx.doi.org/10.12737/1900623.
Pełny tekst źródłaStreszczenie:
The monograph examines the features of risk management in the field of information technology, describes the methodology for building the organizational structure of risk management, analyzes the sequence of steps to establish risk control, pays great attention to the methods and tools of risk management in IT. It provides information about strategic and tactical risks, as well as project risks, and examines the nuances of launching and controlling risk management in IT.
It is intended for a wide range of specialists whose activities are associated with risks in the field of IT, for teachers, as well as for students of enlarged groups of training areas and specialties "Computer Science and Computer Engineering", "Information Security" and "Electronics, radio engineering and communication systems".
10
Davdiev, Kurban, i Ayub Omarov. Repair of cars and engines: final qualifying work. ru: INFRA-M Academic Publishing LLC., 2022. http://dx.doi.org/10.12737/1014616.
Pełny tekst źródłaStreszczenie:
The general provisions concerning the design of production sites of an auto repair enterprise are outlined, the features of the design of production sites of auto repair production are described. The main goals and objectives of the completion of the final qualification work by students of secondary educational institutions, the sequence of its development are indicated. The structure of the calculation and explanatory note, compiled during the performance of the final qualification work on the design of production sites for the repair of various facilities and for the disassembly and assembly of assembly units, is considered in detail.
The issues of technological calculations of production sites are considered in detail. The features of the design of production sites of classes I, II and III are indicated, differences in the organization of work of these sites are shown, the features of calculations used in the development of their projects are given, examples of calculations are given. The development and design of the design part are considered. The measures for occupational health and safety, fire safety and environmental protection are listed. The appendices provide extensive reference material used in the development of the final qualifying work.
It is intended for students of secondary vocational educational institutions in the preparation of final qualifying work on the subject "Repair of cars and engines" in the specialty 23.02.03 "Maintenance and repair of cars" and university students in the course work and final qualifying work on the subject "Organization of car repair".
Części książek na temat "Sequence Feature"
1
Anselmetti, B., A. Chep, K. Mawussi i F. Villeneuve. "Feature-State Approach for Operation Sequence Generation". W Integrated Design and Manufacturing in Mechanical Engineering, 93–102. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5588-5_10.
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Saeys, Yvan, i Yves Van de Peer. "Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection". W Knowledge Discovery and Emergent Complexity in Bioinformatics, 107–18. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-71037-0_7.
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Faraggiana, R., F. Castelli, M. Gerbaldi i M. Floquet. "The LI I 6708 Feature in CP Stars". W Upper Main Sequence Stars with Anomalous Abundances, 451–53. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4714-6_70.
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Maitzen, H. M., i H. Hensberge. "The Variability of the λ5200 Feature in CP2 Stars". W Upper Main Sequence Stars with Anomalous Abundances, 183–87. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4714-6_29.
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5
Bailer, Werner. "A Feature Sequence Kernel for Video Concept Classification". W Lecture Notes in Computer Science, 359–69. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17832-0_34.
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Byrne, Charles J. "Feature Diameter as a Function of Sequence Number". W The Moon's Largest Craters and Basins, 15–20. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-22032-1_3.
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Yang, Yong, Longbing Cao i Li Liu. "Time-Sensitive Feature Mining for Temporal Sequence Classification". W PRICAI 2010: Trends in Artificial Intelligence, 315–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-15246-7_30.
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Dai, Jingchao, Kaiqi Yuan, Yuexiang Xie i Ying Shen. "Feature-Aware Attentive Convolutional Neural Network for Sequence Processing". W Knowledge Science, Engineering and Management, 313–25. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-29563-9_28.
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Ren, Jiadong, Changzhen Hu, Kunsheng Wang i Dongmei Zhang. "Software Fault Feature Clustering Algorithm Based on Sequence Pattern". W Web Information Systems and Mining, 439–47. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-05250-7_46.
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Tangirala, Karthik, Nic Herndon i Doina Caragea. "Community Detection-Based Feature Construction for Protein Sequence Classification". W Bioinformatics Research and Applications, 331–42. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-19048-8_28.
Pełny tekst źródłaStreszczenia konferencji na temat "Sequence Feature"
1
Chan, Patrick P. K., Xian Hu, Lili Zhao, Daniel S. Yeung, Dapeng Liu i Lei Xiao. "Convolutional Neural Networks based Click-Through Rate Prediction with Multiple Feature Sequences". W Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. California: International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/277.
Pełny tekst źródłaStreszczenie:
Convolutional Neural Network (CNN) achieved satisfying performance in click-through rate (CTR) prediction in recent studies. Since features used in CTR prediction have no meaningful sequence in nature, the features can be arranged in any order. As CNN learns the local information of a sample, the feature sequence may influence its performance significantly. However, this problem has not been fully investigated. This paper firstly investigates whether and how the feature sequence affects the performance of the CNN-based CTR prediction method. As the data distribution of CTR prediction changes with time, the best current sequence may not be suitable for future data. Two multi-sequence models are proposed to learn the information provided by different sequences. The first model learns all sequences using a single feature learning module, while each sequence is learnt individually by a feature learning module in the second one. Moreover, a method of generating a set of embedding sequences which aims to consider the combined influence of all feature pairs on feature learning is also introduced. The experiments are conducted to demonstrate the effectiveness and stability of our proposed models in the offline and online environment on both the benchmark Avazu dataset and a real commercial dataset.
2
Kim, Yong Se, Eric Wang, Choong Soo Lee i Hyung Min Rho. "Feature-Based Machining Precedence Reasoning and Sequence Planning". W ASME 1998 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1998. http://dx.doi.org/10.1115/detc98/cie-5707.
Pełny tekst źródłaStreszczenie:
Abstract This paper presents a feature-based method to support machining sequence planning. Precedence relations among machining operations are systematically generated based on geometric information, tolerance specifications, and machining expertise. The feature recognition method using Alternating Sum of Volumes With Partitioning (ASVP) Decomposition is applied to obtain a Form Feature Decomposition (FFD) of a part model. Form features are classified into a taxonomy of atomic machining features, to which machining process information has been associated. Geometry-based precedence relations between features are systematically generated using the face dependency information obtained by ASVP Decomposition and the features’ associated machining process information. Multiple sets of precedence relations are generated as alternative precedence trees, based on the feature types and machining process considerations. These precedence trees are further enhanced with precedence relations from tolerance specifications and machining expertise. Machining sequence planning is performed for each of these precedence trees, applying a matrix-based method to reduce the search space while minimizing the number of tool changes. The precedence trees may then be evaluated based on machining cost and other criteria. The precedence reasoning module and operation sequence planning module are currently being implemented within a comprehensive Computer-Aided Process Planning system.
3
Caragea, Cornelia, Adrian Silvescu i Prasenjit Mitra. "Protein Sequence Classification Using Feature Hashing". W 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2011. http://dx.doi.org/10.1109/bibm.2011.91.
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Lan, Yihua, Haozheng Ren, Cunhua Li, Xuefeng Zhao i Zhifang Min. "Feature Based Sequence Image Stitching Method". W 2010 International Conference on Computational Intelligence and Software Engineering (CiSE). IEEE, 2010. http://dx.doi.org/10.1109/cise.2010.5677208.
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Kobayashi, Takumi. "Feature Sequence Representation Via Slow Feature Analysis For Action Classification". W British Machine Vision Conference 2017. British Machine Vision Association, 2017. http://dx.doi.org/10.5244/c.31.125.
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Bhujle, Hemalata. "Feature-preserving 3D fluorescence image sequence denoising". W the Tenth Indian Conference. New York, New York, USA: ACM Press, 2016. http://dx.doi.org/10.1145/3009977.3009983.
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Ravaut, Frederic, i Georges Stamon. "Image sequence analysis and face feature extraction". W Electronic Imaging '97, redaktorzy Georges G. Grinstein i Robert F. Erbacher. SPIE, 1997. http://dx.doi.org/10.1117/12.270328.
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Chen, Mei, Qingmei Xiao, Kazuyuki Matsumoto i Xin Luo. "Detecting Repeating Pattern in Fingerprint Feature Sequence". W 2015 Fifth International Conference on Instrumentation & Measurement, Computer, Communication and Control (IMCCC). IEEE, 2015. http://dx.doi.org/10.1109/imccc.2015.396.
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Wang, Xianwang, Qing Zhang, Ruigang Yang, Brent Seales i Melody Carswell. "Feature-based texture mapping from video sequence". W I3D08: Symposium on Interactive 3D Graphics and Games. New York, NY, USA: ACM, 2008. http://dx.doi.org/10.1145/1342250.1357018.
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CHOU, WEI-YAO, TUN-WEN PAI, JIM ZONE-CHANG LAI, WEN-SHYONG TZOU, MARGARET DAH-TSYR CHANG, HAO-TENG CHANG, WEI-YI CHOU i TAN-CHI FAN. "MULTIPLE INDEXING SEQUENCE ALIGNMENT FOR GROUP FEATURE IDENTIFICATION". W Proceedings of the 3rd Annual RECOMB Workshop. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2008. http://dx.doi.org/10.1142/9781848162525_0019.
Pełny tekst źródłaRaporty organizacyjne na temat "Sequence Feature"
1
Tao, Yang, Amos Mizrach, Victor Alchanatis, Nachshon Shamir i Tom Porter. Automated imaging broiler chicksexing for gender-specific and efficient production. United States Department of Agriculture, grudzień 2014. http://dx.doi.org/10.32747/2014.7594391.bard.
Pełny tekst źródłaStreszczenie:
Extending the previous two years of research results (Mizarch, et al, 2012, Tao, 2011, 2012), the third year’s efforts in both Maryland and Israel were directed towards the engineering of the system. The activities included the robust chick handling and its conveyor system development, optical system improvement, online dynamic motion imaging of chicks, multi-image sequence optimal feather extraction and detection, and pattern recognition. Mechanical System Engineering The third model of the mechanical chick handling system with high-speed imaging system was built as shown in Fig. 1. This system has the improved chick holding cups and motion mechanisms that enable chicks to open wings through the view section. The mechanical system has achieved the speed of 4 chicks per second which exceeds the design specs of 3 chicks per second. In the center of the conveyor, a high-speed camera with UV sensitive optical system, shown in Fig.2, was installed that captures chick images at multiple frames (45 images and system selectable) when the chick passing through the view area. Through intensive discussions and efforts, the PIs of Maryland and ARO have created the protocol of joint hardware and software that uses sequential images of chick in its fall motion to capture opening wings and extract the optimal opening positions. This approached enables the reliable feather feature extraction in dynamic motion and pattern recognition. Improving of Chick Wing Deployment The mechanical system for chick conveying and especially the section that cause chicks to deploy their wings wide open under the fast video camera and the UV light was investigated along the third study year. As a natural behavior, chicks tend to deploy their wings as a mean of balancing their body when a sudden change in the vertical movement was applied. In the latest two years, this was achieved by causing the chicks to move in a free fall, in the earth gravity (g) along short vertical distance. The chicks have always tended to deploy their wing but not always in wide horizontal open situation. Such position is requested in order to get successful image under the video camera. Besides, the cells with checks bumped suddenly at the end of the free falling path. That caused the chicks legs to collapse inside the cells and the image of wing become bluer. For improving the movement and preventing the chick legs from collapsing, a slowing down mechanism was design and tested. This was done by installing of plastic block, that was printed in a predesign variable slope (Fig. 3) at the end of the path of falling cells (Fig.4). The cells are moving down in variable velocity according the block slope and achieve zero velocity at the end of the path. The slop was design in a way that the deacceleration become 0.8g instead the free fall gravity (g) without presence of the block. The tests showed better deployment and wider chick's wing opening as well as better balance along the movement. Design of additional sizes of block slops is under investigation. Slops that create accelerations of 0.7g, 0.9g, and variable accelerations are designed for improving movement path and images.
2
KellerLynn, Katie. John Muir National Historic Site: Geologic resources inventory report. National Park Service, grudzień 2021. http://dx.doi.org/10.36967/nrr-2288497.
Pełny tekst źródłaStreszczenie:
Geologic Resources Inventory reports provide information and resources to help park managers make decisions for visitor safety, planning and protection of infrastructure, and preservation of natural and cultural resources. Information in GRI reports may also be useful for interpretation. This report synthesizes discussions from a scoping meeting held in 2007 and a follow-up conference call in 2020. Chapters of this report discuss the geologic heritage, geologic features and processes, and geologic resource management issues of John Muir National Historic Site. Guidance for resource management and information about the previously completed GRI map data is also provided. A GRI map poster (separate product) illustrate the GRI map data. Geologic features, processes, and resource management issues identified include the Great Valley sequence, an unconformity, the Martinez Formation, the San Andreas Fault, an anticline, fluvial features and processes, erosion, flooding, slope movements, earthquakes, climate change, and paleontological resources.
3
Clark, Todd E., Gergely Ganics i Elmar Mertens. Constructing fan charts from the ragged edge of SPF forecasts. Federal Reserve Bank of Cleveland, listopad 2022. http://dx.doi.org/10.26509/frbc-wp-202236.
Pełny tekst źródłaStreszczenie:
We develop a model that permits the estimation of a term structure of both expectations and forecast uncertainty for application to professional forecasts such as the Survey of Professional Forecasters (SPF). Our approach exactly replicates a given data set of predictions from the SPF (or a similar forecast source) without measurement error. Our model captures fixed horizon and fixed-event forecasts, and can accommodate changes in the maximal forecast horizon available from the SPF. The model casts a decomposition of multi-period forecast errors into a sequence of forecast updates that may be partially unobserved, resulting in a multivariate unobserved components model. In our empirical analysis, we provide quarterly term structures of expectations and uncertainty bands. Our preferred specification features stochastic volatility in forecast updates, which improves forecast performance and yields model estimates of forecast uncertainty that vary over time. We conclude by constructing SPF-based fan charts for calendar-year forecasts like those published by the Federal Reserve. Replication files are available at https://github.com/elmarmertens/ClarkGanicsMertensSPFfancharts.
4
Slattery, S. R., P. J. Barnett, A. J. M. Pugin, D. R. Sharpe, D. Goodyear, R E Gerber, S. Holysh i S. Davies. Tunnel-channel complexes in the Zephyr area, Ontario: potential high-yield aquifers. Natural Resources Canada/CMSS/Information Management, 2023. http://dx.doi.org/10.4095/331410.
Pełny tekst źródłaStreszczenie:
In south-central Ontario, tunnel channels are primary targets for groundwater exploration due to their potential to contain confined, water-bearing, coarse-grained sediment fills. Despite extensive hydrogeologic and geologic exploration within these features, a comprehensive depositional model that illustrates the spatial distribution of coarse- and fine- grained sediment in tunnel-channel complexes is absent. Work in the Zephr area, north of ORM, presents new subsurface data to improve understanding of this geologic setting and to add to geologic models of these channel systems. Findings result from combined geology, sedimentology, geophysics (seismic profiling) and sediment drilling (mud rotary and continuous core) to better our understanding the shallow channel setting north of ORM, including: 1) spatial distribution of coarse- and fine-grained sediments in tunnel-channels; 2) the architecture of tunnel-channel sequences in confluence zones. Preferred aquifer targets aquifer units in the Zephyr area are identified in areas of channel confluence and channel bends. Channel aquifers are confined by 3.9 to 28.5 m thick deposits of rhythmically bedded silt and clay.
5
Gutnick, David, i David L. Coplin. Role of Exopolysaccharides in the Survival and Pathogenesis of the Fire Blight Bacterium, Erwinia amylovora. United States Department of Agriculture, wrzesień 1994. http://dx.doi.org/10.32747/1994.7568788.bard.
Pełny tekst źródłaStreszczenie:
Fireblight, a disease of apples and pears, is caused by Erwinia amylovora. Mutants of E. amylovora that do not produce the extreacellular polysaccharide (EPS), amylovoran, are avirulent. A similar EPS, stewartan, is produced by E. stewartii, which caused Stewart's wilt of corn, and which has also been implicated in the virulence of this strain. Both stewartan and amylovoran are type 1 capsular polysaccharides, typified by the colanic acid slime produced by Escherichia coli. Extracellular polysaccharide slime and capsules are important for the virulence of bacterial pathogens of plants and animals and to enhance their survival and dissemination outside of the host. The goals of this project were to examine the importance of polysaccharide structure on the pathogenicity and survival properties of three pathogenic bacteria: Erwinia amylovora, Erwinia stewartii and Escherichia coli. The project was a collaboration between the laboratories of Dr. Gutnick (PI, E. coli genetics and biochemistry), Dr. Coplin (co-PI, E. stewartii genetics) and Dr. Geider (unfunded collaborator, E. amylovora genetics and EPS analysis). Structural analysis of the EPSs, sequence analysis of the biosynthetic gene clusters and site-directed mutagenesis of individual cps and ams genes revealed that the three gene clusters shared common features for polysaccharide polymerization, translocation, and precursor synthesis as well as in the modes of transcriptional regulation. Early EPS production resulted in decreased virulence, indicating that EPS, although required for pathogenicity, is anot always advantageous and pathogens must regulate its production carefully.
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Davidson, Irit, Hsing-Jien Kung i Richard L. Witter. Molecular Interactions between Herpes and Retroviruses in Dually Infected Chickens and Turkeys. United States Department of Agriculture, styczeń 2002. http://dx.doi.org/10.32747/2002.7575275.bard.
Pełny tekst źródłaStreszczenie:
Tumors in commercial poultry are caused mainly by infection with avian herpes and retroviruses, the herpesvirus Marek's disease virus (MDV) and the retroviruses, reticuloendotheliosis (REV), lymphoid leukosis, subgroups A-I and J (ALV and ALV-J) in chickens, or Iymphoprolipherative disease (LPDV) in turkeys. Infection with one virus aggravates the clinical outcome of birds that are already infected by another oncogenic virus. As these viruses do not interfere for infection, MDV and one or more retroviruses can infect the same flock, the same bird and the same cell. While infecting the same cell, herpes and retroviruses might interact in at least three ways: a) Integration of retrovirus genomes, or genomic fragments (mainly the LTR) into MDV;b) alteration of LTR-driven expression of retroviral genes by MDV immediate- early genes, and c) by herpesvirus induced cellular transcriptional factors. The first type of molecular interaction have been demonstrated to happen efficiently in vitro by Dr. Kung, in cases multiple infection of cell cultures with MDV and REV or MDV and ALV. Moreover, Dr. Witter showed that an in vitro-created recombinant, RM1, had altered in vitro replication and in vivo biological properties. A more comprehensive characterization of RM1 was carried out in the present project. We sought to highlight whether events of such integrations occur also in the bird, in vivo. For that, we had first to determine the prevalence of dually-infected individual birds in commercial flocks, as no systematic survey has been yet reported. Surprisingly, about 25% of the commercial flocks infected with avian oncogenic viruses had a multiple virus infection and 5% of the total samples ana lysed had multiple virus sequences. Then, we aimed to evaluate and characterize biologically and molecularly the resulting recombinants, if formed, and to analyse the factors that affect these events (virus strains, type and age of birds and time interval between the infection with both viruses). The perception of retrovirus insertions into herpesviruses in vivo is not banal, as the in vivo and in vitro systems differ in the viral-target cells, lymphocytes or fibroblasts, in the MDV-replicative type, transforming or productive, and the immune system presence. We realized that previous methods employed to study in vitro created recombinant viruses were not adequate for the study of samples taken directly from the bird. Therefore, the Hot Spot-combined PCR was developed based on the molecularly known RM1 virus. Also, the PFGE that was used for tissue cultured-MDV separation was inefficient for separating MDV from organs, but useful with feather tips as a source of bird original MDV. Much attention was dedicated now to feathers, because if a recombinant virus would be formed in vivo, its biological significance would be evident by horizontal dissemination through the feathers. Major findings were: a) not only in vitro, but also in vivo MDV and retrovirus co-infections lead to LTR integrations into MDV. That was shown by the detection of chimeric molecules. These appeared in low quantities and as quasispecies, thus interfering with sequence analysis of cloned gel-purified chimeric molecules. Mainly inserts were located in the repeat long MDV fragments. In field birds chimeric molecules were detected at a lower frequency (2.5%) than in experimentally infected birds (30-50%). These could be transmitted experimentally to another birds by inoculation with chimeric molecules containing blood. Several types of chimeric molecules were formed, and same types were detected in birds infected by a second round. To reproduce viral integrations, in vivo infection trials were done with field inoculate that contained both viruses, but the chimeric molecule yield was undetectable.
7
Ostersetzer-Biran, Oren, i Alice Barkan. Nuclear Encoded RNA Splicing Factors in Plant Mitochondria. United States Department of Agriculture, luty 2009. http://dx.doi.org/10.32747/2009.7592111.bard.
Pełny tekst źródłaStreszczenie:
Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for a small number of genes required in organellar genome expression and respiration. Yet, the vast majority of the organellar proteins are encoded by nuclear genes, thus necessitating complex mechanisms to coordinate the expression and accumulation of proteins encoded by the two remote genomes. Many organellar genes are interrupted by intervening sequences (introns), which are removed from the primary presequences via splicing. According to conserved features of their sequences these introns are all classified as “group-II”. Their splicing is necessary for organellar activity and is dependent upon nuclear-encoded RNA-binding cofactors. However, to-date, only a tiny fraction of the proteins expected to be involved in these activities have been identified. Accordingly, this project aimed to identify nuclear-encoded proteins required for mitochondrial RNA splicing in plants, and to analyze their specific roles in the splicing of group-II intron RNAs. In non-plant systems, group-II intron splicing is mediated by proteins encoded within the introns themselves, known as maturases, which act specifically in the splicing of the introns in which they are encoded. Only one mitochondrial intron in plants has retained its maturaseORF (matR), but its roles in organellar intron splicing are unknown. Clues to other proteins required for organellar intron splicing are scarce, but these are likely encoded in the nucleus as there are no other obvious candidates among the remaining ORFs within the mtDNA. Through genetic screens in maize, the Barkan lab identified numerous nuclear genes that are required for the splicing of many of the introns within the plastid genome. Several of these genes are related to one another (i.e. crs1, caf1, caf2, and cfm2) in that they share a previously uncharacterized domain of archaeal origin, the CRM domain. The Arabidopsis genome contains 16 CRM-related genes, which contain between one and four repeats of the domain. Several of these are predicted to the mitochondria and are thus postulated to act in the splicing of group-II introns in the organelle(s) to which they are localized. In addition, plant genomes also harbor several genes that are closely related to group-II intron-encoded maturases (nMats), which exist in the nucleus as 'self-standing' ORFs, out of the context of their cognate "host" group-II introns and are predicted to reside within the mitochondria. The similarity with known group-II intron splicing factors identified in other systems and their predicted localization to mitochondria in plants suggest that nuclear-encoded CRM and nMat related proteins may function in the splicing of mitochondrial-encoded introns. In this proposal we proposed to (i) establish the intracellular locations of several CRM and nMat proteins; (ii) to test whether mutations in their genes impairs the splicing of mitochondrial introns; and to (iii) determine whether these proteins are bound to the mitochondrial introns in vivo.
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Ostersetzer-Biran, Oren, i Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, styczeń 2016. http://dx.doi.org/10.32747/2016.7604267.bard.
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Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evolved from a common alpha-proteobacterial ancestor, notable genomic reorganizations have occurred in the mtDNAs of different eukaryotic lineages. Plant mtDNAs are notably larger and more variable in size (ranging from 70~11,000 kbp in size) than the mrDNAs in higher animals (16~19 kbp). Another unique feature of plant mitochondria includes the presence of both circular and linear DNA fragments, which undergo intra- and intermolecular recombination. DNA-seq data indicate that such recombination events result with diverged mitochondrial genome configurations, even within a single plant species. One common plant phenotype that emerges as a consequence of altered mtDNA configuration is cytoplasmic male sterility CMS (i.e. reduced production of functional pollen). The maternally-inherited male sterility phenotype is highly valuable agriculturally. CMS forces the production of F1 hybrids, particularly in predominantly self-pollinating crops, resulting in enhanced crop growth and productivity through heterosis (i.e. hybrid vigor or outbreeding enhancement). CMS lines have been implemented in some cereal and vegetables, but most crops still lack a CMS system. This work focuses on the analysis of the molecular basis of CMS. We also aim to induce nuclear or organellar induced male-sterility in plants, and to develop a novel approach for fertility restoration. Our work focuses on Brassicaceae, a large family of flowering plants that includes Arabidopsis thaliana, a key model organism in plant sciences, as well as many crops of major economic importance (e.g., broccoli, cauliflower, cabbage, and various seeds for oil production). In spite of the genomic rearrangements in the mtDNAs of plants, the number of genes and the coding sequences are conserved among different mtDNAs in angiosperms (i.e. ~60 genes encoding different tRNAs, rRNAs, ribosomal proteins and subunits of the respiratory system). Yet, in addition to the known genes, plant mtDNAs also harbor numerous ORFs, most of which are not conserved among species and are currently of unknown function. Remarkably, and relevant to our study, CMS in plants is primarily associated with the expression of novel chimericORFs, which likely derive from recombination events within the mtDNAs. Whereas the CMS loci are localized to the mtDNAs, the factors that restore fertility (Rfs) are identified as nuclear-encoded RNA-binding proteins. Interestingly, nearly all of the Rf’s are identified as pentatricopeptide repeat (PPR) proteins, a large family of modular RNA-binding proteins that mediate several aspects of gene expression primarily in plant organelles. In this project we proposed to develop a system to test the ability of mtORFs in plants, which are closely related to known CMS factors. We will induce male fertility in various species of Brassicaceae, and test whether a down-relation in the expression of the recombinantCMS-genes restores fertility, using synthetically designed PPR proteins.
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McElwain, Terry F., Eugene Pipano, Guy H. Palmer, Varda Shkap, Stephn A. Hines i Wendy C. Brown. Protection of Cattle against Babesiosis: Immunization against Babesia bovis with an Optimized RAP-1/Apical Complex Construct. United States Department of Agriculture, wrzesień 1999. http://dx.doi.org/10.32747/1999.7573063.bard.
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Previous research and current efforts at control of babesiosis fall short of meeting the needs of countries where the disease is endemic, such as Israel, as well as the needs of exporting countries and countries bordering on endemic areas, such as the U.S. Our long-term goal is to develop improved methods of immunization against bovine babesiosis based on an understanding of the molecular mechanisms of immune protection and parasite targets of a protective immune response. In our previous BARD project, we established the basis for focusing on rhoptry antigens as components of a subunit vaccine against bovine babesiosis, and for additional research to better characterize rhoptry associated protein-1 (RAP-1) as a target of protective immunity. In this continuation BARD project, our objectives were to [1] optimize the immune response against RAP-1, and [2] identify additional rhoptry candidate vaccine antigens. The entire locus encoding B. bovis RAP-1 was sequenced, and the rap-1 open reading frame compared among several strains. Unlike B. bigemina, in which multiple gene copies with variant domains encode RAP-1, the B. bovis RAP-1 locus contains only two identical genes which are conserved among strains. Through testing of multiple truncated constructs of rRAP-1, one or more immunodominant T cell epitopes were mapped to the amino terminal half of RAP-1. At least one linear and one conformational B cell epitope have been demonstrated in the same amino terminal construct, which in B. bigemina RAP-1 also contains an epitope recognized by neutralizing antibody. The amine terminal half of the molecule represents the most highly conserved part of the gene family and contains motifs conserved broadly among the apicomplexa. In contrast, the carboxy terminal half of B. bovis RAP-1 is less well conserved and contains multiple repeats encoding a linear B cell epitope potentially capable of inducing an ineffective, T cell independent, type 2 immune response. Therefore, we are testing an amino terminal fragment of RAP-1 (RAP-1N) in an immunization trial in cattle. Cattle have beer immunized with RAP-1N or control antigen, and IL-12 with Ribi adjuvant. Evaluation of the immune response is ongoing, and challenge with virulent B. bovis will occur in the near future. While no new rhoptry antigens were identified, our studies did identify and characterize a new spherical body antigen (SBP3), and several heat shock proteins (HSP's). The SBP3 and HSP21 antigens stimulate T cells from immune cattle and are considered new vaccine candidates worthy of further testing. Overall, we conclude that a single RAP-1 vaccine construct representing the conserved amino terminal region of the molecule should be sufficient for immunization against all strains of B. bovis. While results of the ongoing immunization trial will direct our next research steps, results at this time are consistent with our long term goal of designing a subunit vaccine which contains only the epitopes relevant to induction of protective immunity. Parallel studies are defining the mechanisms of protective immunity. Apicomplexan protozoa, including babesiosis and malaria, cause persistent diseases for which control is inadequate. The apical organelles are defining features of these complex protozoa, and have been conserved through the evolutionary process, Past and current BARD projects on babesiosis have established the validity and potential of exploiting these conserved organelles in developing improved control methods applicable to all apicomplexan diseases.
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Dickman, Martin B., i Oded Yarden. Genetic and chemical intervention in ROS signaling pathways affecting development and pathogenicity of Sclerotinia sclerotiorum. United States Department of Agriculture, lipiec 2015. http://dx.doi.org/10.32747/2015.7699866.bard.
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Abstract: The long-term goals of our research are to understand the regulation of sclerotial development and pathogenicity in S. sclerotior11111. The focus in this project was on the elucidation of the signaling events and environmental cues involved in the regulation of these processes, utilizing and continuously developing tools our research groups have established and/or adapted for analysis of S. sclerotiorum, Our stated objectives: To take advantage of the recent conceptual (ROS/PPs signaling) and technical (amenability of S. sclerotiorumto manipulations coupled with chemical genomics and next generation sequencing) developments to address and extend our fundamental and potentially applicable knowledge of the following questions concerning the involvement of REDOX signaling and protein dephosphorylation in the regulation of hyphal/sclerotial development and pathogenicity of S. sclerotiorum: (i) How do defects in genes involved in ROS signaling affect S. sclerotiorumdevelopment and pathogenicity? (ii) In what manner do phosphotyrosinephosphatases affect S. sclerotiorumdevelopment and pathogenicity and how are they linked with ROS and other signaling pathways? And (iii) What is the nature of activity of newly identified compounds that affect S. sclerotiori,111 growth? What are the fungal targets and do they interfere with ROS signaling? We have met a significant portion of the specific goals set in our research project. Much of our work has been published. Briefly. we can summarize that: (a) Silencing of SsNox1(NADPHoxidase) expression indicated a central role for this enzyme in both virulence and pathogenic development, while inactivation of the SsNox2 gene resulted in limited sclerotial development, but the organism remained fully pathogenic. (b) A catalase gene (Scatl), whose expression was highly induced during host infection is involved in hyphal growth, branching, sclerotia formation and infection. (c) Protein tyrosine phosphatase l (ptpl) is required for sclerotial development and is involved in fungal infection. (d) Deletion of a superoxidedismutase gene (Sssodl) significantly reduced in virulence on both tomato and tobacco plants yet pathogenicity was mostly restored following supplementation with oxalate. (e) We have participated in comparative genome sequence analysis of S. sclerotiorumand B. cinerea. (f) S. sclerotiorumexhibits a potential switch between biotrophic and necrotrophic lifestyles (g) During plant microbe interactions cell death can occur in both resistant and susceptible events. Non pathogenic fungal mutants S. sclerotior111n also cause a cell death but with opposing results. We investigated PCD in more detail and showed that, although PCD occurs in both circumstances they exhibit distinctly different features. The mutants trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive (resistant) response. Using electron and fluorescence microscopy, chemical effectors and reverse genetics, we have established that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this interaction Thus the control of cell death, dictated by the plant (autophagy) סr the fungus (apoptosis), is decisive to the outcome of certain plant microbe interactions. In addition to the time and efforts invested towards reaching the specific goals mentioned, both Pls have initiated utilizing (as stated as an objective in our proposal) state of the art RNA-seq tools in order to harness this technology for the study of S. sclerotiorum. The Pls have met twice (in Israel and in the US), in order to discuss .נחd coordinate the research efforts. This included a working visit at the US Pls laboratory for performing RNA-seq experiments and data analysis as well as working on a joint publication (now published). The work we have performed expands our understanding of the fundamental biology (developmental and pathogenic) of S. sclerotioז111וז. Furthermore, based on our results we have now reached the conclusion that this fungus is not a bona fide necrotroph, but can also display a biotrophic lifestyle at the early phases of infection. The data obtained can eventually serve .נ basis of rational intervention with the disease cycle of this pathogen.