Reversible fingerprinting for genomic information

This is a post-peer-review, pre-copyedit version of an article published in Multimedia Tools and Applications. The final authenticated version is available online at: https://doi.org/10.1007/s11042-019-08496-yNew genome sequencing technologies have simplified the generation of genomic data, making them more common but in turn a likely target of attack. Security strategies have been devised such as restricting the amount of information that can be queried or using new encryption techniques. These solutions might not be enough if the entire file has to be shared, as the recipient might leak the accessible information. This contribution addresses this issue using watermarking. Each read in a genomic file is modified depending on its content and a secret key. This allows generating different watermarked instances of the original file. Each watermark acts as a fingerprint: if a leak occurs, the unique modifications of the instance points to who originated the unauthorized publication. Using the key, the modifications can be undone. This allows sharing a leak-discouraging version with which the relevance of a file can be assessed, and can be reversed to the original if needed.Peer ReviewedPostprint (author's final draft

Diversity across Seasons of Culturable Pseudomonas from a Desiccation Lagoon in Cuatro Cienegas, Mexico.

Cuatro Cienegas basin (CCB) is a biodiversity reservoir within the Chihuahuan desert that includes several water systems subject to marked seasonality. While several studies have focused on biodiversity inventories, this is the first study that describes seasonal changes in diversity within the basin. We sampled Pseudomonas populations from a seasonally variable water system at four different sampling dates (August 2003, January 2004, January 2005, and August 2005). A total of 70 Pseudomonas isolates across seasons were obtained, genotyped by fingerprinting (BOX-PCR), and taxonomically characterized by 16S rDNA sequencing. We found 35 unique genotypes, and two numerically dominant lineages (16S rDNA sequences) that made up 64% of the sample: P. cuatrocienegasensis and P. otitidis. We did not recover genotypes across seasons, but lineages reoccurred across seasons; P. cuatrocienegasensis was isolated exclusively in winter, while P. otitidis was only recovered in summer. We statistically show that taxonomic identity of isolates is not independent of the sampling season, and that winter and summer populations are different. In addition to the genetic description of populations, we show exploratory measures of growth rates at different temperatures, suggesting physiological differences between populations. Altogether, the results indicate seasonal changes in diversity of free-living aquatic Pseudomonas populations from CCB

Functional proteomics.

Background: With the increase in the number of genome sequencing projects, there is a concomitant exponential growth in the number of protein sequences whose function is still unknown. Functional proteomics constitutes an emerging research area in the proteomic field whose approaches are addressed towards two major targets: the elucidation of the biological function of unknown proteins and the definition of cellular mechanisms at the molecular level. Methods: The identification of interacting proteins in stable complexes in vivo is essentially achieved by affinity-based procedures. The basic idea is to express the protein of interest with a suitable tag to be used as a bait to fish its specific partners out from a cellular extract. Individual components within the multi-protein complex can then be identified by mass spectrometric methodologies. Results and conclusions: The association of an unknown protein with partners belonging to a specific protein complex involved in a particular mechanism is strongly suggestive of the biological function of the protein. Moreover, the identification of protein partners interacting with a given protein will lead to the description of cellular mechanisms at the molecular level. The next goal will be to generate animal models bearing a tagged form of the bait protein

Security strategies in genomic files

There are new mechanisms to sequence and process the genomic code, discovering thus diagnostic tools and treatments. The file for a sequenced genome can reach hundreds of gigabytes. Thus, for further studies, we need new means to compress the information and a standardized representation to simplify the development of new tools. The ISO standardization group MPEG has used its expertise in compressing multimedia content to compress genomic information and develop its ´MPEG-G standard’. Given the sensitivity of the data, security is a major identified requirement. This thesis proposes novel technologies that assure the security of both the sequenced data and its metadata. We define a container-based file format to group data, metadata, and security information at the syntactical level. It includes new features like grouping multiple results in a same file to simplify the transport of whole studies. We use the granularity of the encoder’s output to enhance security. The information is represented in units, each dedicated to a specific region of the genome, which allows to provide encryption and signature features on a region base. We analyze the trade-off between security and an even more fine-grained approach and prove that apparently secure settings can be insecure: if the file creator may encrypt only specific elements of a unit, cross-checking unencrypted information permits to infer encrypted content. Most of the proposals for MPEG-G coming from other research groups and companies focused on data compression and representation. However, the need was recognized to find a solution for metadata encoding. Our proposal was included in the standard: an XML-based solution, separated in a core specification and extensions. It permits to adapt the metadata schema to the different genomic repositories' frameworks, without importing requirements from one framework to another. To simplify the handling of the resulting metadata, we define profiles, i.e. lists of extensions that must be present in a given framework. We use XML signature and XML encryption for metadata security. The MPEG requirements also concern access rules. Our privacy solutions limit the range of persons with access and we propose access rules represented with XACML to convey under which circumstances a user is granted access to a specific action among the ones specified in MPEG-G's API, e.g. filtering data by attributes. We also specify algorithms to combine multiple rules by defining default behaviors and exceptions. The standard’s security mechanisms protect the information only during transport and access. Once the data is obtained, the user could publish it. In order to identify leakers, we propose an algorithm that generates unique, virtually undetectable variations. Our solution is novel as the marking can be undone (and the utility of the data preserved) if the corresponding secret key is revealed. We also show how to combine multiple secret keys to avoid collusion. The API retained for MPEG-G considers search criteria not present in the indexing tables, which highlights shortcomings. Based on the proposed MPEG-G API we have developed a solution. It is based on a collaboration framework where the different users' needs and the patient's privacy settings result in a purpose-built file format that optimizes query times and provides privacy and authenticity on the patient-defined genomic regions. The encrypted output units are created and indexed to optimize query times and avoid rarely used indexing fields. Our approach resolves the shortcomings of MPEG-G's indexing strategy. We have submitted our technologies to the MPEG standardization committee. Many have been included in the final standard, via merging with other proposals (e.g. file format), discussion (e.g. security mechanisms), or direct acceptance (e.g. privacy rules).Hi han nous mètodes per la seqüenciació i el processament del codi genòmic, permetent descobrir eines de diagnòstic i tractaments en l’àmbit mèdic. El resultat de la seqüenciació d’un genoma es representa en un fitxer, que pot ocupar centenars de gigabytes. Degut a això, hi ha una necessitat d’una representació estandarditzada on la informació és comprimida. Dins de la ISO, el grup MPEG ha fet servir la seva experiència en compressió de dades multimèdia per comprimir dades genòmiques i desenvolupar l'estàndard MPEG-G, sent la seguretat un dels requeriments principals. L'objectiu de la tesi és garantir aquesta seguretat (encriptant, firmant i definint regles d¿ accés) tan per les dades seqüenciades com per les seves metadades. El primer pas és definir com transportar les dades, metadades i paràmetres de seguretat. Especifiquem un format de fitxer basat en contenidors per tal d'agrupar aquets elements a nivell sintàctic. La nostra solució proposa noves funcionalitats com agrupar múltiples resultats en un mateix fitxer. Pel que fa la seguretat de dades, la nostra proposta utilitza les propietats de la sortida del codificador. Aquesta sortida és estructurada en unitats, cadascuna dedicada a una regió concreta del genoma, permetent una encriptació i firma de dades específica a la unitat. Analitzem el compromís entre seguretat i un enfocament de gra més fi demostrant que configuracions aparentment vàlides poden no ser-ho: si es permet encriptar sols certes sub-unitats d'informació, creuant els continguts no encriptats, podem inferir el contingut encriptat. Quant a metadades, proposem una solució basada en XML separada en una especificació bàsica i en extensions. Podem adaptar l'esquema de metadades als diferents marcs de repositoris genòmics, sense imposar requeriments d’un marc a un altre. Per simplificar l'ús, plantegem la definició de perfils, és a dir, una llista de les extensions que han de ser present per un marc concret. Fem servir firmes XML i encriptació XML per implementar la seguretat de les metadades. Les nostres solucions per la privacitat limiten qui té accés a les dades, però no en limita l’ús. Proposem regles d’accés representades amb XACML per indicar en quines circumstàncies un usuari té dret d'executar una de les accions especificades a l'API de MPEG-G (per exemple, filtrar les dades per atributs). Presentem algoritmes per combinar regles, per tal de poder definir casos per defecte i excepcions. Els mecanismes de seguretat de MPEG-G protegeixen la informació durant el transport i l'accés. Una vegada l’usuari ha accedit a les dades, les podria publicar. Per tal d'identificar qui és l'origen del filtratge de dades, proposem un algoritme que genera modificacions úniques i virtualment no detectables. La nostra solució és pionera, ja que els canvis es poden desfer si el secret corresponent és publicat. Per tant, la utilitat de les dades és mantinguda. Demostrem que combinant varis secrets, podem evitar col·lusions. L'API seleccionada per MPEG-G, considera criteris de cerca que no són presents en les taules d’indexació. Basant-nos en aquesta API, hem desenvolupat una solució. És basada en un marc de col·laboració, on la combinació de les necessitats dels diferents usuaris i els requeriments de privacitat del pacient, es combinen en una representació ad-hoc que optimitza temps d’accessos tot i garantint la privacitat i autenticitat de les dades. La majoria de les nostres propostes s’han inclòs a la versió final de l'estàndard, fusionant-les amb altres proposes (com amb el format del fitxer), demostrant la seva superioritat (com amb els mecanismes de seguretat), i fins i tot sent acceptades directament (com amb les regles de privacitat)

Security strategies in genomic files

There are new mechanisms to sequence and process the genomic code, discovering thus diagnostic tools and treatments. The file for a sequenced genome can reach hundreds of gigabytes. Thus, for further studies, we need new means to compress the information and a standardized representation to simplify the development of new tools. The ISO standardization group MPEG has used its expertise in compressing multimedia content to compress genomic information and develop its ´MPEG-G standard’. Given the sensitivity of the data, security is a major identified requirement. This thesis proposes novel technologies that assure the security of both the sequenced data and its metadata. We define a container-based file format to group data, metadata, and security information at the syntactical level. It includes new features like grouping multiple results in a same file to simplify the transport of whole studies. We use the granularity of the encoder’s output to enhance security. The information is represented in units, each dedicated to a specific region of the genome, which allows to provide encryption and signature features on a region base. We analyze the trade-off between security and an even more fine-grained approach and prove that apparently secure settings can be insecure: if the file creator may encrypt only specific elements of a unit, cross-checking unencrypted information permits to infer encrypted content. Most of the proposals for MPEG-G coming from other research groups and companies focused on data compression and representation. However, the need was recognized to find a solution for metadata encoding. Our proposal was included in the standard: an XML-based solution, separated in a core specification and extensions. It permits to adapt the metadata schema to the different genomic repositories' frameworks, without importing requirements from one framework to another. To simplify the handling of the resulting metadata, we define profiles, i.e. lists of extensions that must be present in a given framework. We use XML signature and XML encryption for metadata security. The MPEG requirements also concern access rules. Our privacy solutions limit the range of persons with access and we propose access rules represented with XACML to convey under which circumstances a user is granted access to a specific action among the ones specified in MPEG-G's API, e.g. filtering data by attributes. We also specify algorithms to combine multiple rules by defining default behaviors and exceptions. The standard’s security mechanisms protect the information only during transport and access. Once the data is obtained, the user could publish it. In order to identify leakers, we propose an algorithm that generates unique, virtually undetectable variations. Our solution is novel as the marking can be undone (and the utility of the data preserved) if the corresponding secret key is revealed. We also show how to combine multiple secret keys to avoid collusion. The API retained for MPEG-G considers search criteria not present in the indexing tables, which highlights shortcomings. Based on the proposed MPEG-G API we have developed a solution. It is based on a collaboration framework where the different users' needs and the patient's privacy settings result in a purpose-built file format that optimizes query times and provides privacy and authenticity on the patient-defined genomic regions. The encrypted output units are created and indexed to optimize query times and avoid rarely used indexing fields. Our approach resolves the shortcomings of MPEG-G's indexing strategy. We have submitted our technologies to the MPEG standardization committee. Many have been included in the final standard, via merging with other proposals (e.g. file format), discussion (e.g. security mechanisms), or direct acceptance (e.g. privacy rules).Hi han nous mètodes per la seqüenciació i el processament del codi genòmic, permetent descobrir eines de diagnòstic i tractaments en l’àmbit mèdic. El resultat de la seqüenciació d’un genoma es representa en un fitxer, que pot ocupar centenars de gigabytes. Degut a això, hi ha una necessitat d’una representació estandarditzada on la informació és comprimida. Dins de la ISO, el grup MPEG ha fet servir la seva experiència en compressió de dades multimèdia per comprimir dades genòmiques i desenvolupar l'estàndard MPEG-G, sent la seguretat un dels requeriments principals. L'objectiu de la tesi és garantir aquesta seguretat (encriptant, firmant i definint regles d¿ accés) tan per les dades seqüenciades com per les seves metadades. El primer pas és definir com transportar les dades, metadades i paràmetres de seguretat. Especifiquem un format de fitxer basat en contenidors per tal d'agrupar aquets elements a nivell sintàctic. La nostra solució proposa noves funcionalitats com agrupar múltiples resultats en un mateix fitxer. Pel que fa la seguretat de dades, la nostra proposta utilitza les propietats de la sortida del codificador. Aquesta sortida és estructurada en unitats, cadascuna dedicada a una regió concreta del genoma, permetent una encriptació i firma de dades específica a la unitat. Analitzem el compromís entre seguretat i un enfocament de gra més fi demostrant que configuracions aparentment vàlides poden no ser-ho: si es permet encriptar sols certes sub-unitats d'informació, creuant els continguts no encriptats, podem inferir el contingut encriptat. Quant a metadades, proposem una solució basada en XML separada en una especificació bàsica i en extensions. Podem adaptar l'esquema de metadades als diferents marcs de repositoris genòmics, sense imposar requeriments d’un marc a un altre. Per simplificar l'ús, plantegem la definició de perfils, és a dir, una llista de les extensions que han de ser present per un marc concret. Fem servir firmes XML i encriptació XML per implementar la seguretat de les metadades. Les nostres solucions per la privacitat limiten qui té accés a les dades, però no en limita l’ús. Proposem regles d’accés representades amb XACML per indicar en quines circumstàncies un usuari té dret d'executar una de les accions especificades a l'API de MPEG-G (per exemple, filtrar les dades per atributs). Presentem algoritmes per combinar regles, per tal de poder definir casos per defecte i excepcions. Els mecanismes de seguretat de MPEG-G protegeixen la informació durant el transport i l'accés. Una vegada l’usuari ha accedit a les dades, les podria publicar. Per tal d'identificar qui és l'origen del filtratge de dades, proposem un algoritme que genera modificacions úniques i virtualment no detectables. La nostra solució és pionera, ja que els canvis es poden desfer si el secret corresponent és publicat. Per tant, la utilitat de les dades és mantinguda. Demostrem que combinant varis secrets, podem evitar col·lusions. L'API seleccionada per MPEG-G, considera criteris de cerca que no són presents en les taules d’indexació. Basant-nos en aquesta API, hem desenvolupat una solució. És basada en un marc de col·laboració, on la combinació de les necessitats dels diferents usuaris i els requeriments de privacitat del pacient, es combinen en una representació ad-hoc que optimitza temps d’accessos tot i garantint la privacitat i autenticitat de les dades. La majoria de les nostres propostes s’han inclòs a la versió final de l'estàndard, fusionant-les amb altres proposes (com amb el format del fitxer), demostrant la seva superioritat (com amb els mecanismes de seguretat), i fins i tot sent acceptades directament (com amb les regles de privacitat)

Beyond DNA: Epigenetics and Proteomics in Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to approximate the age of biological sample donors, differentiate between DNA of monozygotic twins, distinguish between natural and synthesized DNA, and identify body fluid sources from forensic material. Proteomic research studies indicate that mass spectrometry can be used to identify biological matrices and tissue sources from forensic biological samples without compromising DNA evidence. The demand for improved forensic techniques necessitates further research into these fields and, specifically, how the associated methods can be used in forensic science

Security strategies in genomic files

There are new mechanisms to sequence and process the genomic code, discovering thus diagnostic tools and treatments. The file for a sequenced genome can reach hundreds of gigabytes. Thus, for further studies, we need new means to compress the information and a standardized representation to simplify the development of new tools. The ISO standardization group MPEG has used its expertise in compressing multimedia content to compress genomic information and develop its ´MPEG-G standard’. Given the sensitivity of the data, security is a major identified requirement. This thesis proposes novel technologies that assure the security of both the sequenced data and its metadata. We define a container-based file format to group data, metadata, and security information at the syntactical level. It includes new features like grouping multiple results in a same file to simplify the transport of whole studies. We use the granularity of the encoder’s output to enhance security. The information is represented in units, each dedicated to a specific region of the genome, which allows to provide encryption and signature features on a region base. We analyze the trade-off between security and an even more fine-grained approach and prove that apparently secure settings can be insecure: if the file creator may encrypt only specific elements of a unit, cross-checking unencrypted information permits to infer encrypted content. Most of the proposals for MPEG-G coming from other research groups and companies focused on data compression and representation. However, the need was recognized to find a solution for metadata encoding. Our proposal was included in the standard: an XML-based solution, separated in a core specification and extensions. It permits to adapt the metadata schema to the different genomic repositories' frameworks, without importing requirements from one framework to another. To simplify the handling of the resulting metadata, we define profiles, i.e. lists of extensions that must be present in a given framework. We use XML signature and XML encryption for metadata security. The MPEG requirements also concern access rules. Our privacy solutions limit the range of persons with access and we propose access rules represented with XACML to convey under which circumstances a user is granted access to a specific action among the ones specified in MPEG-G's API, e.g. filtering data by attributes. We also specify algorithms to combine multiple rules by defining default behaviors and exceptions. The standard’s security mechanisms protect the information only during transport and access. Once the data is obtained, the user could publish it. In order to identify leakers, we propose an algorithm that generates unique, virtually undetectable variations. Our solution is novel as the marking can be undone (and the utility of the data preserved) if the corresponding secret key is revealed. We also show how to combine multiple secret keys to avoid collusion. The API retained for MPEG-G considers search criteria not present in the indexing tables, which highlights shortcomings. Based on the proposed MPEG-G API we have developed a solution. It is based on a collaboration framework where the different users' needs and the patient's privacy settings result in a purpose-built file format that optimizes query times and provides privacy and authenticity on the patient-defined genomic regions. The encrypted output units are created and indexed to optimize query times and avoid rarely used indexing fields. Our approach resolves the shortcomings of MPEG-G's indexing strategy. We have submitted our technologies to the MPEG standardization committee. Many have been included in the final standard, via merging with other proposals (e.g. file format), discussion (e.g. security mechanisms), or direct acceptance (e.g. privacy rules).Hi han nous mètodes per la seqüenciació i el processament del codi genòmic, permetent descobrir eines de diagnòstic i tractaments en l’àmbit mèdic. El resultat de la seqüenciació d’un genoma es representa en un fitxer, que pot ocupar centenars de gigabytes. Degut a això, hi ha una necessitat d’una representació estandarditzada on la informació és comprimida. Dins de la ISO, el grup MPEG ha fet servir la seva experiència en compressió de dades multimèdia per comprimir dades genòmiques i desenvolupar l'estàndard MPEG-G, sent la seguretat un dels requeriments principals. L'objectiu de la tesi és garantir aquesta seguretat (encriptant, firmant i definint regles d¿ accés) tan per les dades seqüenciades com per les seves metadades. El primer pas és definir com transportar les dades, metadades i paràmetres de seguretat. Especifiquem un format de fitxer basat en contenidors per tal d'agrupar aquets elements a nivell sintàctic. La nostra solució proposa noves funcionalitats com agrupar múltiples resultats en un mateix fitxer. Pel que fa la seguretat de dades, la nostra proposta utilitza les propietats de la sortida del codificador. Aquesta sortida és estructurada en unitats, cadascuna dedicada a una regió concreta del genoma, permetent una encriptació i firma de dades específica a la unitat. Analitzem el compromís entre seguretat i un enfocament de gra més fi demostrant que configuracions aparentment vàlides poden no ser-ho: si es permet encriptar sols certes sub-unitats d'informació, creuant els continguts no encriptats, podem inferir el contingut encriptat. Quant a metadades, proposem una solució basada en XML separada en una especificació bàsica i en extensions. Podem adaptar l'esquema de metadades als diferents marcs de repositoris genòmics, sense imposar requeriments d’un marc a un altre. Per simplificar l'ús, plantegem la definició de perfils, és a dir, una llista de les extensions que han de ser present per un marc concret. Fem servir firmes XML i encriptació XML per implementar la seguretat de les metadades. Les nostres solucions per la privacitat limiten qui té accés a les dades, però no en limita l’ús. Proposem regles d’accés representades amb XACML per indicar en quines circumstàncies un usuari té dret d'executar una de les accions especificades a l'API de MPEG-G (per exemple, filtrar les dades per atributs). Presentem algoritmes per combinar regles, per tal de poder definir casos per defecte i excepcions. Els mecanismes de seguretat de MPEG-G protegeixen la informació durant el transport i l'accés. Una vegada l’usuari ha accedit a les dades, les podria publicar. Per tal d'identificar qui és l'origen del filtratge de dades, proposem un algoritme que genera modificacions úniques i virtualment no detectables. La nostra solució és pionera, ja que els canvis es poden desfer si el secret corresponent és publicat. Per tant, la utilitat de les dades és mantinguda. Demostrem que combinant varis secrets, podem evitar col·lusions. L'API seleccionada per MPEG-G, considera criteris de cerca que no són presents en les taules d’indexació. Basant-nos en aquesta API, hem desenvolupat una solució. És basada en un marc de col·laboració, on la combinació de les necessitats dels diferents usuaris i els requeriments de privacitat del pacient, es combinen en una representació ad-hoc que optimitza temps d’accessos tot i garantint la privacitat i autenticitat de les dades. La majoria de les nostres propostes s’han inclòs a la versió final de l'estàndard, fusionant-les amb altres proposes (com amb el format del fitxer), demostrant la seva superioritat (com amb els mecanismes de seguretat), i fins i tot sent acceptades directament (com amb les regles de privacitat).Postprint (published version

Genetic diversity of medically important and emerging Candida species causing invasive infection

Background: Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.Methods: We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C (R) system, as well as by the sequencing of rDNA ITS. the presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.Results: Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C (R) profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.Conclusions: Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo, Dept Med, Lab Especial Micol LEMI, Disciplina Infectol, BR-04039032 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, Disciplina Biol Celular, BR-04039032 São Paulo, BrazilUniv Fed Alfenas, Inst Ciencias Biomed, Dept Microbiol & Imunol, Alfenas, MG, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, Lab Genom Evolut & Biocomplexidade, BR-04039032 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Med, Lab Especial Micol LEMI, Disciplina Infectol, BR-04039032 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, Disciplina Biol Celular, BR-04039032 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, Lab Genom Evolut & Biocomplexidade, BR-04039032 São Paulo, BrazilFAPESP: 2007/08575-1Web of Scienc

Pseudomonas daroniae sp. nov. and Pseudomonas dryadis sp. nov., isolated from pedunculate oak affected by acute oak decline in the UK

Twenty-two cream-coloured bacterial strains were isolated from oak trees affected by acute oak decline (AOD) in Southern England. Isolates were Gram-negative, motile, slightly curved rods, aerobic, non-spore-forming, catalase positive and oxidase positive. 16S rRNA gene sequence analysis placed the strains in two separate phylogenetic clusters in the Pseudomonas straminea group, with Pseudomonas flavescens as the closest phylogenetic relative. Multilocus sequence analyses of the gyrB, rpoD and rpoB genes supported the delineation of the strains into two separate taxa, which could be differentiated phenotypically and chemotaxonomically from each other, and their closest relatives. Average nucleotide identity and in silico DNA-DNA hybridization values revealed percentages of genome similarity below the species threshold (95 and 70 %, respectively) between the two taxa and the closest relatives, confirming their novel species status. Therefore, on the basis of this polyphasic approach we propose two novel Pseudomonas species, Pseudomonasdaroniae sp. nov. (type strain FRB 228T=LMG 31087T=NCPPB 4672T) and Pseudomonasdryadis sp. nov. (type strain FRB 230T=LMG 31087T=NCPPB 4673T)