Percorrer por autor "Branco, Iuliia"
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- Bioinformatics: new tools and applications in life science and personalized medicinePublication . Branco, Iuliia; Choupina, AltinoWhile we have a basic understanding of the functioning of the gene when coding sequences of specific proteins, we feel the lack of information on the role that DNA has on specific diseases or functions of thousands of proteins that are produced. Bioinformatics combines the methods used in the collection, storage, identification, analysis, and correlation of this huge and complex information. All this work produces an “ocean” of information that can only be “sailed” with the help of computerized methods. The goal is to provide scientists with the right means to explain normal biological processes, dysfunctions of these processes which give rise to disease, and approaches that allow the discovery of new medical cures. Recently, sequencing platforms, a large scale of genomes and transcriptomes, have created new challenges not only to the genomics but especially for bioinformatics. The intent of this article is to compile a list of tools and information resources used by scientists to treat information from the massive sequencing of recent platforms to new generations and the applications of this information in different areas of life sciences including medicine.
- Fatores moleculares no metabolismo fundamental de Phytophthora cinnamomiPublication . Ribeiro, Daniel; Branco, Iuliia; Choupina, AltinoPhytophthora cinnamomi é um Oomiceta diploide que vive no solo e é o causador da morte de inúmeras plantas em todo o mundo. Em Portugal a produção de castanheiro europeu encontra-se sobretudo na região norte onde mais de 80% está concentrada principalmente na região de Trás-os-Montes, tornando-se uma fonte económica muito valiosa para a região. A doença da tinta do castanheiro europeu é uma patologia causada principalmente por P. cinnamomi e representa uma ameaça para a preservação do castanheiro europeu (Castanea sativa Miller). O principal objetivo deste trabalho é a identificação de genes que expressam proteínas relacionadas com o metabolismo fundamental de P. cinnamomi, através da utilização de ferramentas bioinformáticas. O genoma deste microrganismo encontra-se depositado na base de dados biológicos NCBI (National Center for Biotechnology Information) e através das sequências desse genoma foram identificadas as ORFs (open reading frames - fases de leitura aberta) que codifiquem para proteínas associadas ao metabolismo fundamental. Com ferramentas bioinformáticas conseguimos ainda predizer a localização subcelular, a estrutura tridimensional, as características físico-químicas e a caracterização dos domínios dessas proteínas.
- In silico characterization of molecular factors involved in metabolism and pathogenicity of Phytophthora cinnamomiPublication . Boughanmi, Mohamed Belhassan; Branco, Iuliia; Choupina, AltinoPhytophthora cinnamomi is classified as one of the most devastating plant pathogens in the world. It has a destructive effect on more than 5000 horticultural and forestry species in the world, and especially on Castanea sativa. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus like organisms which provoke plant diseases via motile zoospores. Control of this organism is considered very challenging because of the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires in-depth knowledge of the cellular and molecular bases of development and metabolism. The aim of this review was to identify molecular factors associated with the metabolism of P. cinnamomi by studying the genes implicated in fundamental metabolism using tools of bioinformatics. Also, some genes involved in pathogenicity will be cited and characterized, such as genes coding for transglycosylases. Genomic sequences of P. cinnamomi were analyzed using an open reading frame (ORF) finder. The identified ORFs products (proteins) were compared to sequences already described and with known functions present in databases such as NCBI and fungi database. In this way, homologous proteins were found, with the respective specific domains, to proteins involved in the metabolism and pathogenicity of Phytophthora ssp.
- In Silico characterization of the Phytopathogenic efector, avr3a, from Phytophthora cinnamomiPublication . Branco, Iuliia; Choupina, AltinoPhytophthora cinnamomi is an Oomycete considered one of the most widespread and destructive pathogens on the planet. Its geographic presence is cosmopolitan and the range of hosts is regarded as one of the largest. This pathogen causes enormous economic damages to important cultures worldwide; this has helped to attract the attention of the scientific community. It is the causal agent of chestnut “ink” disease (Castanea sativa Miller). The chestnut tree has different applications, besides chestnut and wood, it plays an important role in soil ecology and biodiversity. Therefore it is important to know the molecular mechanisms (genes and proteins) that are the basis of the Castanea sativa infestation process by Phytophthora cinnamomi and the nature of the pathogen-host interaction in order to establish strategies to combat and control this parasite. With bioinformatics tools, we were able to identify and characterize the Avr3a gene in genomic sequences of P. cinnamomi deposited in the Databases. This gene encodes a recognized 209 aminoacids, protein in the host cytoplasm where it triggers cell death.
- Phytopathogenic oomycetes: a review focusing on Phytophthora cinnamomi and biotechnological approachesPublication . Lourenço, Darling de Andrade; Branco, Iuliia; Choupina, AltinoThe Phytophthora genus is composed, mainly, of plant pathogens. This genus belongs to the Oomycete class, also known as “pseudo-fungi”, within the Chromista Kingdom. Phytophthora spp. is highlighted due to the signifcant plant diseases that they cause, which represents some of the most economically and cultural losses, such as European chestnut ink disease, which is caused by P. cinnamomi. Currently, there have been four genome assemblies placed at the National Center for Biotechnology Information (NCBI), although the progress to understand and elucidate the pathogenic process of P. cinnamomi by its genome is progressing slowly. In this review paper, we aim to report and discuss the recent fndings related to P. cinnamomi and its genomic information. Our research is based on paper databases that reported probable functions to P. cinnamomi proteins using sequence alignments, bioinformatics, and biotechnology approaches. Some of these proteins studied have functions that are proposed to be involved in the asexual sporulation and zoosporogenesis leading to the host colonization and consequently associated with pathogenicity. Some remarkable genes and proteins discussed here are related to oospore development, inhibition of sporangium formation and cleavage, inhibition of fagellar assembly, blockage of cyst germination and hyphal extension, and bioflm proteins. Lastly, we report some biotechnological approaches using biological control, studies with genome sequencing of P. cinnamomi resistant plants, and gene silencing through RNA interference (iRNA).
- A systematic review about biological control of phytopathogenic Phytophthora cinnamomiPublication . Lourenço, Darling de Andrade; Branco, Iuliia; Choupina, AltinoThe oomycetes of the genus Phytophthora have the most aggressive species for agriculture and forestry, such as Phytophthora sojae which is responsible for soybean root rot, Phytophthora infestans responsible for the potato downy mildew that caused the diaspora in Ireland in the nineteenth-century, and Phytophthora cinnamomi that afects a wide variety of tree species, from avocado in America, trees in Oceania to European chestnut trees. P. cinnamomi reproduces either sexually or asexually and asexual zoospores can live as saprotrophs and subsist in the soil long after death and removal of host plants. Controlling this organism is very challenging for researchers due to the limited range of efective chemical inhibitors. In this work, we present a systematic review of alternatives for biocontrol of Phytophthora in general and P. cinnamomi in particular. Our literature review indicates that Trichoderma spp., mainly Trichoderma harzianum, T. virens, and T. asperellum are very promising fungal species in the control of diferent Phytophthora spp. The Bacillus genus is also very promising in the control and inhibition of several Phytophthoras spp.
- Use of iRNA in the post-transcriptional gene silencing of necrosis-inducing Phytophthora protein 1(NPP1) in Phytophthora cinnamomiPublication . Pascoal‑Ferreira, Patrick; Chahed, Abdessalem; Costa, Rodrigo Arthur Fonseca; Branco, Iuliia; Choupina, AltinoPhytophthora cinnamomi is an Oomycetes associated with soil, this Oomycete is one of the most destructive species of Phytophthora, being responsible for the decline of more than 5000 ornamental, forest, or fruit plants. It can secrete a class of protein NPP1 (Phytophthora necrosis inducing protein 1), responsible for inducing necrosis in leaves and roots of plants, leading to their death. Objective This work will report the characterization of the Phytophthora cinnamomi NPP1 gene responsible for the infec tion of Castanea sativa roots and will characterize the mechanisms of interaction between Phytophthora cinnamomi and Castanea sativa, by gene silencing NPP1 from Phytophthora cinnamomi mediated by RNAi. Methods and results For silencing a part of the coding region of the NPP1 gene, was placed in the sense and antisense directions between an intron and ligated to the integrative vector pTH210. Cassette integration was confrmed by PCR and sequencing on the hygromycin-resistant Phytophthora cinnamomi transformants. Transformants obtained with the silenced gene was used to infect Castanea sativa. Conclusions Plants infected with these transformants showed a great reduction in disease symptoms, confrming iRNA as a potential alternative biological tool in the study of molecular factors, and in the control and management of Phytophthora cinnamomi.