Screening protocol for dysphagia in adults: comparison with videofluoroscopic findings

OBJECTIVES: To compare the videofluoroscopic findings of patients with suspected oropharyngeal dysphagia with the results of a clinical screening protocol. METHODS: A retrospective observational cohort study was conducted on all consecutive patients with suspected oropharyngeal dysphagia between March 2015 and February 2016 who were assigned to receive a videofluoroscopic assessment of swallowing. All patients were first submitted to videofluoroscopy and then to the clinical assessment of swallowing. The clinical assessment was performed within the first 24 hours after videofluoroscopy. The videofluoroscopy results were analyzed regarding penetration/aspiration using an 8-point multidimensional perceptual scale. The accuracy of the clinical protocol was analyzed using the sensitivity, specificity, likelihood ratios and predictive values. RESULTS: The selected sample consisted of 50 patients. The clinical protocol presented a sensitivity of 50% and specificity of 95%, with an accuracy of 88%. “Cough” and “wet-hoarse” vocal quality after/during swallowing were clinical indicators that appeared to correctly identify the presence of penetration/aspiration risk. CONCLUSION: The clinical protocol used in the present study is a simple, rapid and reliable clinical assessment. Despite the absence of a completely satisfactory result, especially in terms of the sensitivity and positive predictive values, we suggest that lower rates of pneumonia can be achieved using a formal dysphagia screening method

Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. © 2014 de Setta et al.; licensee BioMed Central Ltd.151European Commission: Agriculture and Rural Development: Sugar http://ec.europa.eu/agriculture/sugar/index_en.htmKellogg, E.A., Evolutionary history of the grasses (2001) Plant Physiol, 125, pp. 1198-1205Grivet, L., Arruda, P., Sugarcane genomics: depicting the complex genome of an important tropical crop (2001) Curr Opin Plant Biol, 5, pp. 122-127Piperidis, G., Piperidis, N., D'Hont, A., Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane (2010) Mol Genet Genomics, 284, pp. 65-73D'Hont, A., Unraveling the genome structure of polyploids using FISH and GISHexamples of sugarcane and banana (2005) Cytogenet Genome Res, 109, pp. 27-33D'Hont, A., Glaszmann, J.C., Sugarcane genome analysis with molecular markers: a first decade of research (2001) Int Soc Sugar Cane Technol Proc XXIV Congr, pp. 556-559Tomkins, J., Yu, Y., Miller-Smith, H., Frisch, D., Woo, S., Wing, R., A bacterial artificial chromosome library for sugarcane (1999) Theor Appl Genet, 99, pp. 419-424Vettore, L., Silva, F.R., Kemper, E.L., Souza, G.M., Silva, A.M., Ferro, M., Henrique-Silva, F., Monteiro-Vitorello, C.B., Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane (2003) Genome Res, 13, pp. 2725-2735Repbase http://www.girinst.org/repbase/Domingues, D.S., Cruz, G.M.Q., Metcalfe, C.J., Nogueira, F.T.S., Vicentini, R., Alves, C.S., Van Sluys, M.-A., Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns (2012) BMC Genomics, 13, p. 137National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Edwards, R.A., The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes (2008) BMC Bioinformatics, 9, p. 386Keeling, P.L., Myers, A.M., Biochemistry and genetics of starch synthesis (2010) Annu Rev Food Sci Technol, 1, pp. 271-303Phytozome v9.1: Home http://www.phytozome.net/Dias, E.S., Carareto, C.M.A., Ancestral polymorphism and recent invasion of transposable elements in Drosophila species (2012) BMC Evol Biol, 12, p. 119Posada, D., Crandall, K., Intraspecific gene genealogies: trees grafting into networks (2001) Trends Ecol Evol, 16, pp. 37-45Swaminathan, K., Alabady, M.S., Varala, K., De Paoli, E., Ho, I., Rokhsar, D.S., Arumuganathan, A.K., Hudson, M.E., Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses (2010) Genome Biol, 11, pp. R12Zanca, A.S., Vicentini, R., Ortiz-Morea, F.A., Del Bem, L.E., da Silva, M.J., Vincentz, M., Nogueira, F.T., Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane (2010) BMC Plant Biol, 10, p. 260Piriyapongsa, J., Jordan, I.K., A family of human microRNA genes from miniature inverted-repeat transposable elements (2007) PLoS ONE, 2, pp. e203Barrera-Figueroa, B.E., Gao, L., Wu, Z., Zhou, X., Zhu, J., Jin, H., Liu, R., Zhu, J.-K., High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice (2012) BMC Plant Biol, 12, p. 132Nagaki, K., Tsujimoto, H., Sasakuma, T., A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions (1998) Chromosom Res, 6, pp. 295-302Nagaki, K., Neumann, P., Zhang, D., Ouyang, S., Buell, C.R., Cheng, Z., Jiang, J., Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice (2005) Mol Biol Evol, 22, pp. 845-855Vicentini, R., Del Bem, L.E., Van Sluys, M.-A., Nogueira, F., Vincentz, M., Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs (2012) Trop Plant Biol, 5, pp. 199-205Kim, C., Lee, T.-H., Compton, R.O., Robertson, J.S., Pierce, G.J., Paterson, A.H., A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin (2013) Plant Mol Biol, 81, pp. 139-147Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Carpita, N.C., The Sorghum bicolor genome and the diversification of grasses (2009) Nature, 457, pp. 551-556Chang, Y., Gong, L., Yuan, W., Li, X., Chen, G., Li, X., Zhang, Q., Wu, C., Replication protein A (RPA1a) is required for meiotic and somatic DNA repair but is dispensable for DNA replication and homologous recombination in rice (2009) Plant Physiol, 151, pp. 2162-2173Feschotte, C., Transposable elements and the evolution of regulatory networks (2008) Nat Rev Genet, 9, pp. 397-405Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Ming, R., Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes (2010) BMC Genomics, 11, p. 261Garsmeur, O., Charron, C., Bocs, S., Jouffe, V., Samain, S., Couloux, A., Droc, G., D'Hont, A., High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane (2011) New Phytol, 189, pp. 629-642Jannoo, N., Grivet, L., Chantret, N., Garsmeur, O., Glaszmann, J.C., Arruda, P., D'Hont, A., Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome (2007) Plant J, 50, pp. 574-585Figueira, T.R.E.S., Okura, V., da Silva, F.R., da Silva, M.J., Kudrna, D., Ammiraju, J.S.S., Talag, J., Arruda, P., A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome (2012) BMC Res Notes, 5, p. 185Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Gillam, B., The B73 maize genome: complexity, diversity, and dynamics (2009) Science, 326, pp. 1112-1115Tenaillon, M.I., Hufford, M.B., Gaut, B.S., Ross-Ibarra, J., Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians (2011) Genome Biol Evol, 3, pp. 219-229Zhang, J., Yu, C., Krishnaswamy, L., Peterson, T., Transposable Elements as Catalysts for Chromosome Rearrangements (2011) Methods Mol Biol, pp. 315-326. , Totowa, NJ: Humana Press, Birchler JAMa, J., Wing, R.A., Bennetzen, J.L., Jackson, S.A., Plant centromere organization: a dynamic structure with conserved functions (2007) Trends Genet, 23, pp. 134-139D'Hont, A., Grivet, L., Feldmann, P., Rao, S., Berding, N., Glaszmann, J.C., Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics (1996) Mol Gen Genet, 250, pp. 405-413Bao, Y., Wendel, J.F., Ge, S., Multiple patterns of rDNA evolution following polyploidy in Oryza (2010) Mol Phylogenet Evol, 55, pp. 136-142Lynch, M., (2007) The Origins of Genome Architecture, , Sunderland, Massachussetts, USA: Sinauer Associates IncThe map-based sequence of the rice genome (2005) Nature, 436, pp. 793-800. , International Rice Genome Sequencing ProjectLiu, B., Xu, C., Zhao, N., Qi, B., Kimatu, J.N., Pang, J., Han, F., Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement (2009) J Genet Genomics, 36, pp. 519-528Lisch, D., How important are transposons for plant evolution? (2012) Nat Rev Genet, 14, pp. 49-61Udall, J.A., Wendel, J.F., Polyploidy and crop improvement (2006) Crop Sci, 46, pp. S3-S14Varshney, R.K., Graner, A., Sorrells, M.E., Genomics-assisted breeding for crop improvement (2005) Trends Plant Sci, 10, pp. 621-630Menossi, M., Silva-Filho, M.C., Vincentz, M., Van-Sluys, M.-A., Souza, G.M., Sugarcane functional genomics: gene discovery for agronomic trait development (2008) Int J Plant Genomics, 2008, p. 458732. , doi:10.1155/2008/458732Palhares, A.C., Rodrigues-Morais, T.B., Van Sluys, M.-A., Domingues, D.S., Maccheroni, W., Jordão, H., Souza, A.P., Vieira, M.L.C., A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers (2012) BMC Genet, 13, p. 51Andersen, J.R., Lübberstedt, T., Functional markers in plants (2003) Trends Plant Sci, 8, pp. 554-560Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C., Schulman, A., Analysis of plant diversity with retrotransposon-based molecular markers (2011) Heredity (Edinb), 106, pp. 520-530PGML BACMan On The Web: Grasses http://www.plantgenome.uga.edu/bacman/BACManwww.phpRice Genome Annotation Project http://rice.plantbiology.msu.edu/Bowers, J.E., Arias, M.A., Asher, R., Avise, J.A., Ball, R.T., Brewer, G.A., Buss, R.W., Soderlund, C.A., Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses (2005) Proc Natl Acad Sci U S A, 102, pp. 13206-13211Adam-Blondon, A.-F., Bernole, A., Faes, G., Lamoureux, D., Pateyron, S., Grando, M.S., Caboche, M., Chalhoub, B., Construction and characterization of BAC libraries from major grapevine cultivars (2005) Theor Appl Genet, 110, pp. 1363-1371Manetti, M.E., Rossi, M., Cruz, G.M.Q., Saccaro, N.L., Nakabashi, M., Altebarmakian, V., Rodier-Goud, M., Van Sluys, M.A., Mutator system derivatives isolated from sugarcane genome sequence (2012) Trop Plant Biol, 5, pp. 233-243Phrap http://www.phrap.org/RepeatMasker http://www.repeatmasker.org/Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Repbase update, a database of eukaryotic repetitive elements (2005) Cytogenet Genome Res, 110, pp. 462-467Han, Y., Wessler, S.R., MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences (2010) Nucleic Acids Res, 38 (22), pp. e199. , doi: 10.1093/nar/gkq862. Epub 2010 Sep 29Frickey, T., Lupas, A., CLANS: a Java application for visualizing protein families based on pairwise similarity (2004) Bioinformatics, 20, pp. 3702-3704Han, Y., Qin, S., Wessler, S.R., Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes (2013) BMC Genomics, 14, p. 71Keller, O., Kollmar, M., Stanke, M., Waack, S., A novel hybrid gene prediction method employing protein multiple sequence alignments (2011) Bioinformatics, 27, pp. 757-763Majoros, W.H., Pertea, M., Salzberg, S.L., TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders (2004) Bioinformatics, 20, pp. 2878-2879Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Hannick, L.I., Maiti, R., White, O., Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies (2003) Nucleic Acids Res, 31, pp. 5654-5666Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Wortman, J.R., Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to assemble spliced alignments (2008) Genome Biol, 9, pp. R7Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions (2011) Nat Methods, 8, pp. 785-786TMHMM Server v. 2.0 http://www.cbs.dtu.dk/services/TMHMM-2.0/Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., Barrell, B., Artemis: sequence visualization and annotation (2000) Bioinformatics, 16, pp. 944-945UniProt http://www.uniprot.org/InterPro: Protein sequence analysis and classification http://www.ebi.ac.uk/interpro/Conesa, A., Götz, S., Blast2GO: a comprehensive suite for functional analysis in plant genomics (2008) Int J Plant Genomics, 2008, pp. 1-12SUCEST-FUN Project http://sucest-fun.org/MG-RAST: metagenomics analysis server http://metagenomics.anl.gov/KAAS - KEGG automatic annotation server http://www.genome.jp/kegg/kaas/Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods (2011) Mol Biol Evol, 28, pp. 2731-2739Lyons, E., Freeling, M., How to usefully compare homologous plant genes and chromosomes as DNA sequences (2008) Plant J, 53, pp. 661-673Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT (1999) Nucleic Acids Symp Ser, 41, pp. 95-98Geneious - Homepage http://www.geneious.com/Heslop-Harrison, P., Schwarzacher, T., (2000) Practical In Situ Hybridization, , Oxford, UK: BIOS Scientific Publishers LtdAljanabi, S., Forget, L., Dookun, A., An improved and rapid protocol for the isolation of polysaccharide-and polyphenol-free sugarcane DNA (1999) Plant Mol Biol Report, 17, pp. 1-8Maq: Mapping and assembly with qualities http://maq.sourceforge.net/SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/Gasic, K., Hernandez, A., Korban, S.S., RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA (2004) Plant Mol Biol Report, 22 (DECEMBER), pp. 437a-437gLi, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Durbin, R., The sequence Alignment/Map format and SAMtools (2009) Bioinformatics, 25, pp. 2078-2079Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice (1994) Nucleic Acids Res, 22, pp. 4673-4680Bandelt, H.J., Forster, P., Röhl, A., Median-joining networks for inferring intraspecific phylogenies (1999) Mol Biol Evol, 16, pp. 37-48Paterson, A.H., Freeling, M., Tang, H., Wang, X., Insights from the comparison of plant genome sequences (2010) Annu Rev Plant Biol, 61, pp. 349-37