CleanEST: a database of cleansed EST libraries

The EST division of GenBank, dbEST, is widely used in many applications such as gene discovery and verification of exon–intron structure. However, the use of EST sequences in the dbEST libraries is often hampered by inconsistent terminology used to describe the library sources and by the presence of contaminated sequences. Here, we describe CleanEST, a novel database server that classified dbEST libraries and removes contaminants. We classified all dbEST libraries according to species and sequencing center. In addition, we further classified human EST libraries by anatomical and pathological systems according to eVOC ontologies. For each dbEST library, we provide two different cleansed sequences: ‘pre-cleansed’ and ‘user-cleansed’. To generate pre-cleansed sequences, we cleansed sequences in dbEST by alignment of EST sequences against well-known contamination sources: UniVec, Escherichia coli, mitochondria and chloroplast (for plant). To provide user-cleansed sequences, we built an automatic user-cleansing pipeline, in which sequences of a user-selected library are cleansed on-the-fly according to user-selected options. The server is available at http://cleanest.kobic.re.kr/ and the database is updated monthly

Atitude do consumidor em relação ao pinhão: estratégias para valorização e conservação da espécie Araucaria angustifolia.

Resumo

Ciliary Beating Recovery in Deficient Human Airway Epithelial Cells after Lentivirus Ex Vivo Gene Therapy

Primary Ciliary Dyskinesia is a heterogeneous genetic disease that is characterized by cilia dysfunction of the epithelial cells lining the respiratory tracts, resulting in recurrent respiratory tract infections. Despite lifelong physiological therapy and antibiotics, the lungs of affected patients are progressively destroyed, leading to respiratory insufficiency. Recessive mutations in Dynein Axonemal Intermediate chain type 1 (DNAI1) gene have been described in 10% of cases of Primary Ciliary Dyskinesia. Our goal was to restore normal ciliary beating in DNAI1–deficient human airway epithelial cells. A lentiviral vector based on Simian Immunodeficiency Virus pseudotyped with Vesicular Stomatitis Virus Glycoprotein was used to transduce cultured human airway epithelial cells with a cDNA of DNAI1 driven by the Elongation Factor 1 promoter. Transcription and translation of the transduced gene were tested by RT–PCR and western blot, respectively. Human airway epithelial cells that were DNAI1–deficient due to compound heterozygous mutations, and consequently had immotile cilia and no outer dynein arm, were transduced by the lentivirus. Cilia beating was recorded and electron microscopy of the cilia was performed. Transcription and translation of the transduced DNAI1 gene were detected in human cells treated with the lentivirus. In addition, immotile cilia recovered a normal beat and outer dynein arms reappeared. We demonstrated that it is possible to obtain a normalization of ciliary beat frequency of deficient human airway epithelial cells by using a lentivirus to transduce cells with the therapeutic gene. This preliminary step constitutes a conceptual proof that is indispensable in the perspective of Primary Ciliary Dyskinesia's in vivo gene therapy. This is the first time that recovery of cilia beating is demonstrated in this disease