Nanopore sequencing is the next generation ofsequencing methods which promises to deliver cheaper andmore portable genome sequencing capabilities. A single DNAor RNA strand is passed through a nanopore nested in anartificial membrane with an electric potential applied across it.The nucleotide bases of the helix then interact with the ioniccurrent in the nanopore, resulting in a unique signal that canbe translated into the correct corresponding nucleotide sequence.This project investigated whether features of the raw signal datacould be used as predictive indicators of the duration time ofeach nucleotide base in the nanopore. This is done in orderto segment the signal before translation. The training data setused came from the sequenced DNA molecules of an E. Colibacterium. Distribution candidates were fitted to a histogram ofthe duration data of the training set. Features of the currentsignal and distribution parameters were correlated in orderinvestigate if a linear predictive model could be created. Theresults indicate that the feature zero-crossings is not an optimaloption for construction of a linear model, while the large jumpsand moving variance features often generate linear patterns. The parameter of the Log-logistic distribution had the best fit withthe lowest relative root mean square deviation (rRMSD) of 2.7%. / Nanopore sequencing är nästa generationensmetod för DNA sekvensering som kommer att bidra medbilligare och mer portabla sekvenseringsmöjligheter. Metodeninnebär att en enkelsträngad DNA eller RNA molekyl passerargenom porer i nanostorlek, placerade i ett artificiellt membransamtidigt som en elektrisk potential appliceras över membranet.Nukleotiderna i genmolekylen interagerar med jonströmmen iporen, vilket resulterar i en unik signal som kan översättas tillden korresponderande sekvensen av nukleotider som passerat.Detta projekt gick ut på att undersöka om egenskaper frånsignalen kan användas som predikativa indikatorer för varaktighetensom varje nukleotid befinner sig i membranporen. Dettaför att sedan kunna segmentera signalen före översättningen tillDNA sekvensen. Träningsdata som användes är sekvenserad DNAfrån en E. Coli bakterie. Kandiderande sannolikhetsfördelningaranpassades till ett histogram som beskriver varaktigheten.Egenskaperna och parametrar från fördelningarna korreleradesför att skapa en linjär modell. Resultatet visade att antaletskärningar i x-axeln som signalegenskap inte är det optimalavalet för konstruktion av en linjär modell. Skillnaden mellan två signalvärden som är mindre än en varierbar konstant ochglidande variansen som signalegenskaper genererar ofta linjäramönster. Resultatet visade även att sannolikhetsfördelningen Loglogistichade lägst relativ medelkvadratavvikelse (rRMSD) på 2.7%. / Kandidatexjobb i elektroteknik 2021, KTH, Stockholm

Nanopore DNA sequencing is a novel method forsequencing DNA where an electronic signal is modulated bynucleotides passing through nanosized pores embedded in a mem-brane. While current state-of-the-art solutions employ recurrentneural networks to analyse the signal, temporal convolutionalnetworks have recently been shown to match or outperformrecurrent networks in signal processing tasks. In this project, weinvestigate the performance of temporal convolutional networkson a simplified version of the sequencing task, where thegoal is to predict the nucleotides passing through the pore ateach instance in time, without reconstructing the correspondingDNA sequence. The impact of several network parameters onpredictive performance is analysed to determine an optimalarchitecture. While the implemented networks are shown tobe proficient at predicting nucleotides within the pore, thecurrent implementation is unlikely to outperform state-of-the-art solutions without further improvement. / En nyligen utvecklad metod för att sekvensera DNA innefattar att en elektrisk signal moduleras genom att nukleotider passerar genom porer i nanostorlek. I kommersiella lösningar analyseras denna signal med hjälp av maskininlärning via Recurrent Neural Networks, men en variant av neruala nätverk som kallas Temporal Convolution Networks har nyligen har visat sig ha bättre prestanda jämfört med Recurrent Networks för olika typer av signalbehandlingsproblem. Målet med detta projekt är att undersöka användbarheten av Temporal Convolutional Networks för en förenklad version av DNA-sekvensering, där uppdraget endast är att identifera de nukleotider som passerar genom poren vid varje given tidpunkt, istället för att rekonstruera en komplett DNA-sekvens. För att kunna bestämma en optimal arkitektur på nätverket så undersöks effekten av flera olika parametrar. De implementerade nätverken visas ha god förmåga att klassificera nukleotider, men är troligtvis i behov av ytterligare förbättringar för att kunna konkurrera med nuvarande kommersiella lösningar. / Kandidatexjobb i elektroteknik 2020, KTH, Stockholm

The Human Genome Project (HGP), the name given to the scientific program to map and decode all of human genetic material, has been projected to revolutionize the conduct of biological science in the twenty-first century. For several years before its formation in 1990, a federally-funded, systematic study of the human genome was discussed first in the scientific arena and then in the public arena. The central thesis of this dissertation is that the arguments supporting or rejecting creation of the HGP and the rhetorical devices used to further those arguments had a major influence on the shape the HGP took in 1991. The argumentation used both for and against the creation of the HGP before the public as well as on the border between the public and scientific arenas is studied. The rhetorical devices such as metaphor, narrative, and selective word choices used to further these arguments are also examined. In particular, a rhetorical content analysis was performed on the 1986-1991 argumentation available to the most crucial audience for such persuasion: the members of Congress who ultimately voted for or against the program's funding and its establishment as a part of U.S. science policy. The proponents of the HGP, especially after the first year of public debate, presented their arguments in a wider arena of discussion and presented more and more varied arguments to advocate the project. The opposition raised questions that had for the most part been answered earlier in the debate. Often anti-HGP arguments focused on less effective audiences (scientists instead of members of Congress). Opposition to the project didn't become organized until near the end of the time frame studied, too late to have much of an impact on the outcome of the debate. The rhetorical devices studied served to magnify the impact of arguments used: in particular, the metaphor served as a boundary object to bridge discussions between the scientific and the public arenas. Ultimately the victory in the debate over the establishment of the HGP was awarded to the promulgators of the strongest underlying metaphor--the idealized excitement and profit of exploration of unknown territory--and the benefits to come from filling in and conquering the unknown areas of the human genetic map, territory the U.S. was eager to claim for its own. / Ph. D.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Roman Reddy R. Ganta / Ehrlichia and Anaplasma species are rickettsial organisms which infect a variety of mammalian species. The organisms are transmitted from ticks and are maintained in reservoir hosts. Several pathogens have been identified in recent years as the causative agents for emerging infections in people. One of the primary reservoir hosts for the pathogens is the white tailed deer. In this study, 147 deer blood samples and 37 ticks were evaluated for the prevalence of Ehrlichia/Anaplasma species by TaqMan-based real time amplification assay and DNA sequence analysis. One hundred and thirteen (74%) samples tested positive with the Ehrlichia/Anaplasma genera-specific probe. Further analysis of the samples with the probes specific for human ehrlichiosis agents, E. chaffeensis and E. ewingii identified 4 (2.7%) and 7 (4.7%) positives, respectively. Test positives from 24 randomly selected samples were further evaluated by sequence analysis targeting to a 450 bp segment of 16S rRNA gene. All 24 samples were confirmed as positive for the Ehrlichia GA isolate # 4 (GenBank #U27104.1). DNAs from 37 pools of ticks collected from the white tailed deer were also evaluated. The TaqMan-based real time PCR assay with Anaplasma/Ehrlichia common probe identified 29 (78%) tick pools as positives whereas E. chaffeensis- and E. ewingii-specific probes identified three (8%) and one (3%) positives, respectively. The PCR and sequence analysis of tick samples identified Gram-negative bacteria species which included one endosymbiont of Rickettsia species (one tick pool), one Alcaligenes faecalis strain (three tick pools), five different Pseudomonas species (9 tick pools) and five different uncultured bacteria organisms (7 tick pools). Although the pathogenic potential of the white-tailed deer isolates of Anaplasma and Ehrlichia agents remains to be established, their high prevalence and the presence of human ehrlichiosis pathogens in white-tailed deer is similar to earlier findings. The high prevalence of the deer isolates of Anaplasma and Ehrlichia species demonstrates the need for further assessment of the pathogenic potential of these organisms to people and domestic animals.

本研究從DNA定序產業之美國專利侵權訴訟，了解該產業中廠商的訴訟行為與系爭專利之特性。本研究由商用資料庫取得DNA定序產業之美國專利侵權訴訟共100件及其系爭專利共168件，分析訴訟資訊、訴訟主體資訊(原告及被告)和訴訟客體資訊(系爭專利和被控侵權產品)。本研究也由次級資料中歸類各廠商在DNA定序產業鏈中之位置和其各世代產品技術之發展。由訴訟主體資訊可得知在DNA定序產業中，主要發起美國專利侵權訴訟之廠商為中游的儀器平台廠商，被控專利侵權的廠商也多為具有相同商業模式在同樣產業鏈位置上的競爭者。而由訴訟客體資訊中，除了以產品技術結構定位系爭專利之保護標的和技術特徵外，也從專利的被引證數、專利家族大小、所有權移轉次數、國際分類號分佈等指標比較系爭專利和一組同樣專利權人在相同時間間隔內申請的同技術領域之對照組專利，可發現系爭專利和對照組專利相比屬於較有價值的專利。 / The present research analyzes the U.S. patent infringement cases of the DNA sequencing industry to understand the features of patent-in-suit and litigation behaviors in said industry. The present research obtains 100 U.S. patent infringement cases and 168 patent-in-suit from commercial databases. The litigation history, parties in the litigation (plaintiff and defendant), subject matter of the litigation (the patent-in-suit and the infringing products) are analyzed. The present research identifies the position of different corporate entities in the DNA sequencing industry chain and the development of each generations of DNA sequencing technology. By analyzing the parties in the litigation, the present research identifies that most of the plaintiffs are corporate entities developing sequencing instrument, and most of the defendants are competitiors having the same business model with the plaintiffs. By analyzing subject matter of the litigation, the present research identifies the technical features and subject matter of the patent-in-suit. The present research compares the citation, patent family size, number of ownership transfer and IPC distribution between the patent-in-suit and a control group patents of the same technical field within the same time frame. The patent-in-suit is more valuable than the control group patents.

The field of microbial ecology has just entered a new era of rapid technological development and generation of big data. The high-throughput sequencing techniques presently available provide an opportunity to extensively inventorize the blueprints of life. Now, millions of microbes of natural microbial communities can be studied simultaneously without prior cultivation. New species and new functions (genes) can be discovered just by mining sequencing data. However, there is still a tremendous number of microorganisms not yet examined, nor are the ecosystem functions these carry out. The modern genomic technologies can contribute to solve environmental problems and help us understand ecosystems, but to most efficiently do so, methods need to be continuously optimised.   During my Ph. D. studies, I developed a method to survey eukaryotic microbial diversity with a higher accuracy, and applied various sequencing-based approaches in an attempt to answer questions of importance in environmental research and ecology. In PAPER-I, we developed a set of 18S rRNA gene PCR primers with high taxonomic coverage, meeting the requirements of currently popular sequencing technologies and matching the richness of 18S rRNA reference sequences accumulated so far. In PAPER-II, we conducted the first sequencing-based spatial survey on the combined eukaryotic and bacterial planktonic community in the Baltic Sea to uncover the relationship of microbial diversity and environmental conditions. Here, the 18S primers designed in PAPER-I and a pair of broad-coverage 16S primers were employed to target the rRNA genes of protists and bacterioplankton for amplicon sequencing. In PAPER-III, we integrated metagenomic, metabarcoding, and metatranscriptomic data in an effort to scrutinise the protein synthesis potential (i.e., activity) of microbes in the sediment at a depth of 460 m in the Baltic Sea and, thus, disclosing microbial diversity and their possible ecological functions within such an extreme environment. Lastly, in PAPER-IV, we compared the performance of E. coli culturing, high-throughput sequencing, and portable real-time sequencing in tracking wastewater contamination in an urban stormwater system. From the aspects of cost, mobility and accuracy, we evaluated the usage of sequencing-based approaches in civil engineering, and for the first time, validated the real-time sequencing device in use within water quality monitoring.   In summary, these studies demonstrate how DNA sequencing of microbial communities can be applied in environmental monitoring and ecological research. / <p>Yue Hu was supported by a scholarship from the China Scholarship Council (CSC #201206950024)</p><p>Yue Hu has been publishing papers under the name "Yue O. O. Hu".</p><p>QC 20170403</p>

Infertility is a widespread health problem, caused by the male factor in about half of all cases, and in about a half of the infertile men the cause is unknown. In a significant number of these men, genetic etiology is assumed. Current routine methods of laboratory diagnostics, which include karyotype examination, exclusion of mutations in the CFTR gene, and Y chromosome microdeletions, do not usually reveal the cause of infertility. That is why researchers' efforts aim at detecting mutations in other genes that are causing male infertility. In recent years, animal models have been used to identify many genes necessary for fertility. Based on these findings, 12 candidate genes have been selected (CAPZA3, CDC14B, CDC42, CNTROB, CSNK2A2, GOPC, HOOK1, HRB, OAZ3, ODF1, RIMBP3, SPATA16) that are essential for spermatogenesis. Mouse or rat mutants in these genes are primarily associated with oligoasthenoteratozoospermia, since they are involved in sperm morphogenesis. However, the phenotype spectrum may comprise also azoospermia. The purpose of the thesis was to determine the sequence of the afore mentioned genes in infertile men with impaired spermatogenesis and to reveal presence or absence of pathogenic mutations in these genes, using cDNA and genomic DNA from peripheral blood. The candidate genes were...

O patógeno Xanthomonas axonopodis pv. passiflorae causa a mancha oleosa ou bacteriose do maracujazeiro, uma doença que acarreta prejuízos à cultura em decorrência da baixa produção de frutos, podendo causar a morte das plantas. Uma coleção de 87 isolados deste patovar, oriundos de 22 cidades dos Estados de São Paulo, Minas Gerais e Paraná e do Distrito Federal, foi usada para estudar a diversidade genética por rep-PCR e AFLP. Nove isolados de outros patovares foram incluídos nas análises genéticas. A técnica rep-PCR revelou pouca diversidade entre os isolados do patovar passiflorae, mas diferenciou, claramente, os diferentes patovares. Todavia, a técnica AFLP revelou considerável diversidade genética entre os isolados do patovar passiflorae. A análise molecular da variância mostrou que a maior parte da diversidade (49,4%) se encontra entre as cidades de coleta. O agrupamento gerado com base nos coeficientes de similaridade e os resultados do teste de atribuição pelo programa Structure revelaram clusters genotípicos homogêneos. Isto evidencia que a variação está mais associada à geografia, ou seja, às cidades de coleta, e que o fluxo desses isolados é pequeno. Cinco conjuntos de primers foram desenhados para a detecção do patógeno em plantas. Desses, um conjunto de primers foi desenhado a partir da seqüência intergênica 16S-23S rRNA e se mostrou específico para o patovar passiflorae. Nenhum amplicon foi detectado nos patovares controles. O restante dos primers foi desenhado a partir do seqüenciamento de locos de AFLP, monomórficos para o patovar passiflorae e ausentes nos demais patovares. Estes primers não foram totalmente específicos; no entanto, todos podem ser recomendados para o diagnóstico da mancha oleosa, uma vez que não há registros de outras Xanthomonas em pomares de maracujá. / The pathogen Xanthomonas axonopodis pv. passiflorae is responsible for the bacterial leaf spot of passion fruits, a disease that provokes commercial losses due to low levels of fruit production and even plant death. A group of 87 isolates of this pathovar, collected from 22 localities of São Paulo, Minas Gerais and Paraná States as in the Federal District was used to evaluate the genetic diversity based on rep-PCR and AFLP. Isolates from other nine pathovars were included in the genetic analyses. Low level of genetic diversity was revealed by the rep- PCR technique, which clearly distinguished the different pathovars. However, considerable diversity between isolates of the pathovar passiflorae was revealed by the AFLP technique. The analysis of molecular variance showed that differences between localities contributed to most part of the variance (49.4%). Groups generated based on similarity coefficients as well as results produced by the software Structure assigning isolates to groups, revealed homogeneous genotypic clusters. This confirms that variance is associated with geographic origin e.g. sampling localities, and that flow of isolates is restricted among localities. Five primer sets were designed for pathogen detection in plants; a primer set was designed for PCR amplification of the intergenic sequence 16-23S rRNA, which was shown to be specific to the pathovar passiflorae. No amplicons were detected in the controls. The remaining primers were designed after sequencing AFLP bands that were monomorphic within the pathovar passiflorae but absent in the other pathovars. These primers were not absolutely specific but all could be recommended for diagnosis of leaf spot as there is no report on the occurrence of other Xanthomonas species in passion fruit orchards.

Ácaros fitoseídeos são eficientes predadores de ácaros pragas em algumas culturas. A precisa identificação das espécies é o passo inicial na seleção de inimigos naturais em um projeto de controle biológico. Os ácaros são geralmente identificados com base nas características morfológicas, mas aspectos biológicos e ecológicos, e mais recentemente características moleculares vêm sendo usadas nesse processo. Populações dos fitoseídeos identificados como Euseius citrifolius Denmark & Muma provenientes de Arroio do Meio-RS, Campinas-SP e Petrolina-PE, e Euseius concordis (Chant) procedentes de Arroio do Meio, Jaguariúna-SP, Petrolina, Pontes e Lacerda-MT e Viçosa-MG foram estudados em relação a morfologia, compatibilidade reprodutiva e características moleculares. A caracterização morfológica correspondeu as medições de estruturas de fêmeas e machos. A compatibilidade reprodutiva foi avaliada através de cruzamentos e retrocruzamentos homogâmicos e heterogâmicos. A caracterização molecular foi realizada com o seqüenciamento dos espaços internos transcritos (ITS1 e ITS2) do DNA ribossomal. Relações significativas foram observadas dentro de cada população entre o comprimento médio das setas e as respectivas amplitudes de variação. Ambos os sexos de E. citrifolius de Petrolina e E.concordis de Jaguariúna tiveram algumas setas mais curtas que as demais populações da mesma espécie; esta última diferiu marcadamente da população de Petrolina. A comparação das medições das estruturas de cada população e dos espécimes tipo de E. citrifolius e E. concordis confirmaram a identificação morfológica preliminar das populações ao nível de espécie. Medições de machos resultantes de cruzamentos heterogâmicos indicaram que essas espécies se reproduzem por pseudo-arrenotoquia. Incompatibilidade parcial foi observada nos cruzamentos heterogâmicos envolvendo fêmeas de E. citrifolius de Petrolina; descendentes produziram poucos ovos e inviáveis quando retrocruzadas com machos das populações parentais. Machos de Petrolina produziram descendentes viáveis quando cruzados com fêmeas de Arroio do Meio e Campinas. Não ocorreu oviposição nos cruzamentos e retrocruzamentos heterogâmicos envolvendo fêmeas de E. concordis de Petrolina. Nos cruzamentos heterogâmicos envolvendo machos de Petrolina a oviposição foi reduzida e somente machos (viáveis) foram produzidos. Cruzamentos de fêmeas de Pontes e Lacerda e machos de Jaguariúna e vice-versa produziram somente machos. Entretanto o fluxo gênico entre essas populações seria possível indiretamente, através de cruzamentos entre essas populações e a população de Arroio do Meio. Populações de Arroio do Meio, Jaguariúna, Pontes e Lacerda e Viçosa pertencem a mesma espécie. Maior variação entre as populações foi observada no espaçador ITS1. O seqüenciamento dos espaçadores ITS1 e ITS2 permitiu discriminar entre os grupos de populações identificadas como E. citrifolius de E. concordis. O seqüenciamento dos ITSs pode ser aplicado como uma ferramenta complementar na identificação de fitoseídeos. Apesar do fato de que alguns tipos de diferenças foram sempre observadas nesta tese entre a população de Petrolina identificada preliminarmente como E. concordis, não é conveniente descrever esta população como uma nova espécie, devido a dificuldade em separar indivíduos dessa população daqueles das populações identificadas como E.concordis. Para uma conclusão, é sugerido que outros estudos de cruzamentos sejam conduzidos com populações morfologicamente identificadas como E. concordis coletadas entre Petrolina e Viçosa, e que a caracterização molecular envolvendo o gene citocromo oxidase seja conduzida. / Phytoseiidae mites are efficient predators of pest mites on several crops. Precise identification is the initial step in the selection of natural enemies in a biological control project. Mites are usually identified by their morphology, but biological and ecological aspects and, more recently, molecular characteristics have also been used in this process. Populations of phytoseiid mites identified as Euseius citrifolius Denmark & Muma from Arroio do Meio-RS, Campinas-SP and Petrolina-PE, and E. concordis (Chant) from Arroio do Meio, Jaguariúna-SP, Petrolina Pontes e Lacerda-MT and Viçosa-MG were studied in relation to morphology, reproductive compatibility and molecular characteristics. Morphological characterization corresponded to measurements of structures of females and males. Reproductive compatibility was evaluated by homogamic and heterogamic crosses and backcrosses. Molecular characterization was done by sequencing the internal transcribed spacers of the ribosomal DNA (ITS1 and ITS2). Significant relationships were observed within each population between mean setal lengths and the respective ranges. Both sexes of E. citrifolius from Petrolina and E. concordis from Jaguariúna had some setae shorter than other populations of the same species; the latter differed most markedly from the Petrolina population. A comparison of the measurements of structures for each population and type specimens of E. citrifolius and E. concordis confirmed the preliminary morphological identification of the populations at species level. Measurements of males resulting from heterogamic crosses indicated that both species reproduce by pseudo-arrhenotoky. Partial incompatibility was observed in heterogamic crosses involving females of E. citrifolius from Petrolina; progeny produced just few, unviable eggs when backcrossed with males of the parental populations. Males from Petrolina produced viable offspring when crossed with females from Arroio do Meio or Campinas. No eggs were produced in heterogamic crosses and backcrosses involving females of E. concordis from Petrolina. In heterogamic crosses involving males from Petrolina, oviposition was reduced and only (viable) males were produced. Crosses of females from Pontes e Lacerda and males from Jaguariúna and vice-versa produced only male progeny. However, gene flow between those population could be possible indirectly, through crosses between those populations and Arroio do Meio population. Populations from Arroio do Meio, Jaguariúna, Pontes e Lacerda and Viçosa belong to a same species. Most of the molecular variation between populations was observed in ITS1. The sequencing of ITS1 and ITS2 allowed the discrimination between the group of populations identified as E. citrifolius from that identified as E. concordis. With the information presently available, sequencing of ITSs can be applied as a complementary tool to identify phytoseiids. Despite the fact that some type of differences were always observed in this thesis between the Petrolina population preliminarily identified as E. concordis and the remaining populations, it is not convenient to describe such population as a new species presently, given the difficulty in separating individuals from that population from those of populations identified as E. concordis. For a conclusion, it is suggested that other crossing studies be conducted with populations morphologically identifiable as E. concordis collected between Petrolina and Viçosa, and that the characterization of the cytochrome oxidase gene be conducted.

A cana-de-açúcar é cultivada em diversos países do mundo. O Brasil é atualmente o maior produtor mundial de cana-de-açúcar e o maior exportador dos produtos derivados dessa espécie, tais como açúcar e etanol. A cultura da cana-deaçúcar apresenta muitos problemas fitossanitários que prejudicam a produção, entre eles o causado pelo vírus do mosaico da cana-de-açúcar (Sugarcane mosaic virus, SCMV). O mosaico da cana-de-açúcar vem sendo controlado com o uso de variedades e híbridos resistentes. No entanto, frequentemente notam-se plantas sintomáticas nas avaliações de novos clones de cana-de-açúcar, em viveiros de mudas e plantios comerciais. Diante desse fato, o presente trabalho teve como objetivo realizar a caracterização biológica e molecular de isolados do SCMV que induzem sintomas variados em plantas de cana-de-açúcar plantadas nos municípios de Assis, Piracicaba e Ribeirão Preto, SP. Nove isolados, identificados por causarem sintomas fraco, intermediário e severo de mosaico foram coletados em cada localidade. Um isolado que causa mosaico listrado também foi coletado em Piracicaba. Todos os isolados foram estabelecidos na variedade SP86155. A caracterização molecular foi feita por meio da analise das sequências de nucleotídeos e de amino ácidos deduzidos do gene da proteína capsidial dos isolados. Também foram diferenciados por meio da análise de polimorfismo de comprimento de fragmentos. A caracterização biológica foi realizada por testes de proteção entre alguns dos isolados. As sequências parciais de nucleotídeos e de aminoácidos deduzidos do gene da proteína capsidial de cada isolado foram comparadas entre si e com outras sequências correspondentes de isolados de diferentes regiões geográficas. As identidades das sequências de nucleotídeos variam de 94 a 100%, entre os isolados estudados. Quando as mesmas sequências foram comparadas com as sequências de nucleotídeos do gene da proteína capsidial de outros isolados do SCMV as identidades variaram de 79 a 98%. Para as sequências de amino ácidos deduzidos as identidades variaram de 94 to 100%, entre os isolados estudados e de 81 to 98% quando comparadas com as de outros isolados do SCMV. Análise filogenética agrupou os 10 isolados com outros isolados brasileiros do SCMV (JAU - 1, RIB - 1 e PIR - 2 e FER - 1) e com os isolados dos E.U.A. originalmente denominados estirpes A, B, D e E. Analises de RFLP mostraram que a enzima de restrição HinfI foi a que melhor diferenciou os isolados e por isso permitiu a análise da proteção. As plantas inoculadas com os isolados fracos de Piracicaba, Ribeirão Preto e Assis ficaram protegidas contra a invasão sistêmica dos isolados severos dos mesmos locais e contra o isolado que causa mosaico listrado de Piracicaba. Falhas na proteção ocorreram em plantas infectadas com o isolado Piracicaba intermediário e desafiadas com os isolados Ribeirão Preto severo e Assis severo. Em conjunto esses resultados indicam que os dez isolados estudados são estirpes do SCMV que induzem sintomas diferenciados. / Sugarcane crop is raised in several tropical countries around the world. Brazil is the largest producer of sugarcane, as well as the largest exporter of ethanol and sugar, which are outputs of sugarcane processing. The sugarcane production faces several sanitary problems and among them is the mosaic disease caused by the potyvirus Sugarcane mosaic virus (SCMV). Traditionally, resistant varieties and hybrids are used for the control of SCMV. However, new cases of symptomatic plants have been reported in commercial crops and in seedling production facilities. Based on this fact, the present work aims to do both molecular and biological characterization of isolates of SCMV which causes different symptoms in sugarcane crops in the regions of Assis (SP), Piracicaba (SP) and Ribeirão Preto (SP). Nine isolates identified as causing mild, intermediate and severe mosaic were collected in each of the three areas. One isolate which causes striped mosaic was also collected in the Piracicaba area. All isolates were established in the variety SP86155 by mechanical inoculation. The molecular characterization was done through the analysis of nucleotide and deduced amino acid sequences for the coat protein gene. Likewise the isolates were differentiated through the analysis of restriction fragment length polymorphism (RFLP) for further use on biological characterization through cross protection tests between the isolates. The partial nucleotide and deduced amino acid sequences for the coat protein gene were compared among themselves and with corresponding sequences for other isolates from different geographical regions. The identity of the nucleotide sequences ranged from 94 to 100% among the studied isolates. When compared with the corresponding nucleotide sequences of other isolates of SCMV the identities ranged from 79 to 98%. The identity of the deduced amino acids sequences ranged from 94 to 100% among the studied isolates, and from 81 to 98% when compared with isolates form different geographical regions. Phylogenetic analysis grouped all 10 isolates with other Brazilian isolates do SCMV (JAU-1, RIB-1 e PIR-2 e FER-1), as well as with isolates from the U.S.A, originally named strains A, B, D e E. RFPL analyses pointed out that the restriction enzyme Hinfl did the best differentiation of the isolates and was further used for the evaluation of the cross protection tests. Plants inoculated with mild isolates remained protected against the severe isolates and also against the isolate which causes the stripped mosaic. Fails on cross protection occurred when plants infected with the isolate Piracicaba intermediate were challenged with isolates Ribeirão Preto and Assis severe. Together these data indicate that the 10 studied isolates are strains of SCMV that induce different symptoms.