464 research outputs found
Using ESTs to improve the accuracy of de novo gene prediction
BACKGROUND: ESTs are a tremendous resource for determining the exon-intron structures of genes, but even extensive EST sequencing tends to leave many exons and genes untouched. Gene prediction systems based exclusively on EST alignments miss these exons and genes, leading to poor sensitivity. De novo gene prediction systems, which ignore ESTs in favor of genomic sequence, can predict such "untouched" exons, but they are less accurate when predicting exons to which ESTs align. TWINSCAN is the most accurate de novo gene finder available for nematodes and N-SCAN is the most accurate for mammals, as measured by exact CDS gene prediction and exact exon prediction. RESULTS: TWINSCAN_EST is a new system that successfully combines EST alignments with TWINSCAN. On the whole C. elegans genome TWINSCAN_EST shows 14% improvement in sensitivity and 13% in specificity in predicting exact gene structures compared to TWINSCAN without EST alignments. Not only are the structures revealed by EST alignments predicted correctly, but these also constrain the predictions without alignments, improving their accuracy. For the human genome, we used the same approach with N-SCAN, creating N-SCAN_EST. On the whole genome, N-SCAN_EST produced a 6% improvement in sensitivity and 1% in specificity of exact gene structure predictions compared to N-SCAN. CONCLUSION: TWINSCAN_EST and N-SCAN_EST are more accurate than TWINSCAN and N-SCAN, while retaining their ability to discover novel genes to which no ESTs align. Thus, we recommend using the EST versions of these programs to annotate any genome for which EST information is available. TWINSCAN_EST and N-SCAN_EST are part of the TWINSCAN open source software package
Hybridization in parasites: consequences for adaptive evolution, pathogenesis and public health in a changing world
[No abstract available
Germline Genetic Variants Disturbing the Let-7/LIN28 Double-Negative Feedback Loop Alter Breast Cancer Susceptibility
Previous studies have shown that let-7 can repress the post-transcriptional translation of LIN28, and LIN28 in turn could block the maturation of let-7, forming a double-negative feedback loop. In this study, we investigated the effect of germline genetic variants on regulation of the homeostasis of the let-7/LIN28 loop and breast cancer risk. We initially demonstrated that the T/C variants of rs3811463, a single nucleotide polymorphism (SNP) located near the let-7 binding site in LIN28, could lead to differential regulation of LIN28 by let-7. Specifically, the C allele of rs3811463 weakened let-7–induced repression of LIN28 mRNA, resulting in increased production of LIN28 protein, which could in turn down-regulate the level of mature let-7. This effect was then validated at the tissue level in that the normal breast tissue of individuals with the rs3811463-TC genotype expressed significantly lower levels of let-7 and higher levels of LIN28 protein than those individuals with the rs3811463-TT genotype. Because previous in vitro and ex vivo experiments have consistently suggested that LIN28 could promote cellular transformation, we then systematically evaluated the relationship between rs3811463 as well as other common LIN28 SNPs and the risk of breast cancer in a stepwise manner. The first hospital-based association study (n = 2,300) demonstrated that two SNPs were significantly associated with breast cancer risk, one of which was rs3811463, while the other was rs6697410. The C allele of the rs3811463 SNP corresponded to an increased risk of breast cancer with an odds ratio (OR) of 1.25 (P = 0.0091), which was successfully replicated in a second independent study (n = 1,156) with community-based controls. The combined P-value of the two studies was 8.0×10−5. Taken together, our study demonstrates that host genetic variants could disturb the regulation of the let-7/LIN28 double-negative feedback loop and alter breast cancer risk
Molecular evolution of viral multifunctional proteins: the case of Potyvirus HC-Pro
[EN] Our knowledge on the mode of evolution of the multifunctional viral proteins remains incomplete. To tackle this problem, here, we have investigated the evolutionary dynamics of the potyvirus multifunctional protein HC-Pro, with particular focus on its functional domains. The protein was partitioned into the three previously described functional domains, and each domain was analyzed separately and assembled. We searched for signatures of adaptive evolution and evolutionary dependencies of amino acid sites within and between the three domains using the entire set of available potyvirus sequences in GenBank. Interestingly, we identified strongly significant patterns of co-occurrence of adaptive events along the phylogenetic tree in the three domains. These patterns suggest that Domain I, whose main function is to mediate aphid transmission, has likely been coevolving with the other two domains, which are involved in different functions but all requiring the capacity to bind RNA. By contrast, episodes of positive selection on Domains II and III did not correlate, reflecting a trade-off between their evolvability and their evolutionary dependency likely resulting from their functional overlap. Covariation analyses have identified several groups of amino acids with evidence of concerted variation within each domain, but interdomain significant covariations were only found for Domains II and III, further reflecting their functional overlappingThis work was supported by grants BFU2012-30805 (SFE) and BFU2012-36346 (MAF) from the Spanish Direccio´n General de Investigacio´n Cientı´fica y Te´cnica and by an EMBO Short-Term Fellowship and the Mentoring Program from the Foundation
for Polish Science (BHJ).Hasiów-Jaroszewska, B.; Fares Riaño, MA.; Elena Fito, SF. (2014). Molecular evolution of viral multifunctional proteins: the case of Potyvirus HC-Pro. Journal of Molecular Evolution. 78(1):75-86. https://doi.org/10.1007/s00239-013-9601-0S7586781Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487Atreya CD, Atryea P, Thornbury DW, Pirone TP (1992) Site-directed mutations in the potyvirus HC-Pro gene affect helper component activity, virus accumulation and symptoms expression in infected tobacco plants. Virology 191:106–111Blanc S, López-Moya JJ, Wang R, García-Lampasona S, Thornbury DW, Pirone TP (1997) A specific interaction between coat protein and helper component correlates with aphid transmission of a potyvirus. Virology 231:141–147Blanc S, Ammar ED, García-Lampasona S, Dolja VV, Llave C, Baker J, Pirone TP (1998) Mutations in the potyvirus helper component protein: effects on interactions with virions and aphid stylets. J Gen Virol 79:3119–3122Cantó T, López-Moya JJ, Serra-Yodi MT, Díaz-Ruiz JR, López-Abella D (1995) Different helper component mutations associated with lack of aphid transmissibility in two isolates of potato virus. Phytopathology 85:1519–1524Carrington JC, Freed DD, Sanders TC (1989) Autocatalytic processing of the potyvirus helper component proteinase in Escherichia coli and in vitro. J Virol 63:4459–4463Chung BY, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902Cronin S, Verchot J, Haldeman-Cahill R, Schaad MC, Carrington JC (1995) Long distance movement factor: a transport function of the potyvirus helper component-proteinase. Plant Cell 7:549–559Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797Elena SF, Rodrigo G (2012) Towards and integrated molecular model of plant-virus interactions. Curr Opin Virol 2:713–718Fares MA (2004) SWAPSC: sliding-window analysis procedure to detect selective constraints. Bioinformatics 20:2867–2868Fares MA, McNally D (2006) CAPS: coevolution analysis using protein sequences. Bioinformatics 22:2821–2822Fares MA, Travers AA (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constrains analyses. Genetics 173:9–23Fares MA, Elena SF, Ortiz J, Moya A, Barrio E (2002) A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J Mol Evol 55:509–521Gibbs A, Ohshima K (2010) Potyviruses and the digital revolution. Annu Rev Phytopathol 48:205–223Guo D, Mertis A, Saarma M (1999) Self-association and mapping of interaction domains of helper component of Potato virus A potyvirus. J Gen Virol 80:1127–1131Guo B, Lin J, Ye K (2011) Structure of the autocatalytic cysteine protease domain of potyvirus helper-component proteinase. J Biol Chem 286:21937–21943Haikonen T, Rajamäki ML, Tian YP, Valkonen JPT (2013) Mutation of a short variable region in HC-Pro protein of Potato virus A affects interactions with microtubule-associated protein and induces necrotic responses in tobacco. Mol Plant Microbe Interact 26:721–733Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Hughes AL (2009) Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology 393:127–134Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202Kasschau KD, Carrington JC (1995) Requirement for HC-Pro processing during genome amplification of Tobacco etch potyvirus. Virology 209:268–273Kasschau KD, Carrington JC (2001) Long-distance movement and replication maintenance functions correlate with silencing suppression activity of potyviral HC-Pro. Virology 285:71–81Kasschau KD, Cronin S, Carrington JC (1997) Genome amplification and long-distance movement functions associated with the central domain of Tobacco etch potyvirus helper component-proteinase. Virology 228:251–262Kosakovsky Pond SL, Frost SDW (2005a) DATAMONKEY: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533Kosakovsky Pond SL, Frost SDW (2005b) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SDW (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 23:1891–1901Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu YP, Dojla VV, Calvino LF, López-Moya JJ, Burgyan J (2006) Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25:2768–2780Lalić J, Elena SF (2012) Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus. Heredity 109:71–77Leigh JW, Susko E, Baumgartner M, Roger AJ (2008) Testing congruence in phylogenomic analysis. Syst Biol 57:104–115Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99Llave C, Kasschau KD, Carrington JC (2000) Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway. Proc Natl Acad Sci USA 97:13401–13406Maia S, Haenni AL, Bernardi F (1996) Potyviral HC-Pro: a multifunctional protein. J Gen Virol 77:1335–1341Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463Moroni E, Morra G, Colombo G (2012) Molecular dynamics simulations of Hsp90 with an eye to inhibitor design. Pharmaceuticals 5:944–962Peng YH, Kadoury D, Gaol-On A, Huet H, Wang Y, Raccah B (1998) Mutations in HC-Pro gene of Zucchini yellow mosaic potyvirus: effects on aphid transmission and binding to purified virions. J Gen Virol 79:897–904Plisson C, Drucker M, Blanc S, German-Retana S, Le Gall O, Thomas D, Bron P (2003) Structural characterization of HC-Pro a plant virus multifunctional protein. J Biol Chem 278:23753–23761Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818Revers F, Le Gall O, Candresse T, Maule J (1999) New advances in understanding the molecular biology of plant/potyvirus interaction. Mol Plant Microbe Interact 12:367–376Riechmann JL, Lain S, García JA (1992) Highlights and prospects of potyvirus molecular biology. J Gen Virol 73:1–16Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738Ruiz-Ferrer V, Boskovic J, Alfonso C, Rivas G, Llorca O, López-Abella D, López-Moya JJ (2005) Structural analysis of Tobacco etch potyvirus HC-pro oligomers involved in aphid transmission. J Virol 79:3758–3765Shiboleth YM, Haronsky E, Leibman D, Arazi T, Wassenegger M, Whitham SA, Gaba V, Gal-On A (2007) The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development. J Virol 81:13135–13148Smoot M, Ono K, Ruschelnski J, Wang PL, Ideker T (2011) CYTOSCAPE 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432Syller J (2006) The roles and mechanisms of helper component proteins encoded by potyviruses and caulimoviruses. Physiol Mol Plant Pathol 67:119–130Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739Torres-Barceló C, Martín S, Daròs JA, Elena SF (2008) From hypo- to hypersuppression: effect of amino acid substitutions on the RNA-silencing suppressor activity of Tobacco etch potyvirus HC-Pro. Genetics 180:1039–1049Torres-Barceló C, Daròs JA, Elena SF (2010a) Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus. Mol Biol Evol 27:543–551Torres-Barceló C, Daròs JA, Elena SF (2010b) HC-Pro hypo- and hypersuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro. Arch Virol 155:251–254Urcuqui-Inchima S, Walter J, Drugeon G, German-Retans S, Haeni AL, Candresse T, Bernardi F, Le Gall O (1999) Potyvirus HC-Pro self-interaction in the yeast two hybrid system and delineation of the interaction domain involved. Virology 258:95–99Urcuqui-Inchima S, Maia IG, Arruda P, Haenni AL, Bernardi F (2000) Deletion mapping of the potyviral helper component-proteinase reveals two regions involved in RNA binding. Virology 268:104–111Urcuqui-Inchima S, Haenni AL, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175Varrelmann M, Maiss E, Pilot R, Palkovics L (2007) Use of pentapeptide-insertion scanning mutagenesis for functional mapping of the Plum pox virus helper component proteinase suppressor of gene silencing. J Gen Virol 88:10051015Ward CW, Shukla DD (1991) Taxonomy of potyviruses: current problems and some solutions. Intervirology 32:269–296Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucl Acids Res 35:3375–3382Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503Yap YK, Duangjit J, Panyim S (2009) N-terminal of Papaya ringspot virus type-W (PRSV-W) helper component proteinase (HC-Pro) is essential for PRSV systemic infection in zucchini. Virus Genes 38:461–467Zheng H, Yan F, Lu Y, Sun L, Lin L, Cai L, Hou M, Chen J (2010) Mapping the self-interaction domains of TuMV HC-pro and the subcellular localization of the protein. Virus Genes 42:110–11
Detection and Characterization of CD133+ Cancer Stem Cells in Human Solid Tumours
Osteosarcoma is the most common primary tumour of bone. Solid tumours are made of heterogeneous cell populations, which display different goals and roles in tumour economy. A rather small cell subset can hold or acquire stem potentials, gaining aggressiveness and increasing expectancy of recurrence. The CD133 antigen is a pentaspan membrane glycoprotein, which has been proposed as a cancer stem cell marker, since it has been previously demonstrated to be capable of identifying a cancer initiating subpopulation in brain, colon, melanoma and other solid tumours. Therefore, our aim was to observe the possible presence of cells expressing the CD133 antigen within solid tumour cell lines of osteosarcoma and, then, understand their biological characteristics and performances.In this study, using SAOS2, MG63 and U2OS, three human sarcoma cell lines isolated from young Caucasian subjects, we were able to identify and characterize, among them, CD133+ cells showing the following features: high proliferation rate, cell cycle detection in a G2\M phase, positivity for Ki-67, and expression of ABCG2 transporters. In addition, at the FACS, we were able to observe the CD133+ cell fraction showing side population profile and forming sphere-clusters in serum-free medium with a high clonogenic efficiency.Taken together, our findings lead to the thought that we can assume that we have identified, for the first time, CD133+ cells within osteosarcoma cell lines, showing many features of cancer stem cells. This can be of rather interest in order to design new therapies against the bone cancer
Health information management and perceptions of the quality of care for children with tracheotomy: A qualitative study
The geoaccumulation index and enrichment factor of mercury in mangrove sediment of Port Klang, Selangor, Malaysia.
Mangrove areas are important to the ecosystem. One of its crucial functions is as a sink of pollutants, especially metal ions. However, the accumulation of metals in mangrove sediment can generate negative impacts on plant growth, microbial activity, and soil fertility. Apart from that, the severity of the impact is highly influenced by the type of metal found in the sediment and the quality of sediment itself. One of the metals that have adverse effects on the environment is mercury. The objectives of this study are to determine the concentration and distribution of mercury and to assess the enrichment of mercury in Port Klang mangrove sediment by using geoaccumulation index and enrichment factor. Sediment samples were collected from 30 sampling points that cover Langat River and Klang River estuaries, Lumut Straits, Pulau Klang, and Pulau Indah. During sampling, water parameters such as pH, salinity, electrical conductivity, and total dissolved solids were measured in situ, whereas the total mercury in sediment samples was determined at the laboratory using inductively coupled plasma mass spectrometry. In this study, mercury was found to be concentrated along Lumut Strait especially in the mixing zone near the confluence of Langat River and at the jetty to Pulau Ketam. The geoaccumulation index and enrichment factor (calculated using logarithmized data of the reference element) found that three stations were enriched with mercury. In addition, geoaccumulation index was also observed to be more objective compared to enrichment factor whose results were influenced by the concentration of reference element used
LPS unmasking of Shigella flexneri reveals preferential localisation of tagged outer membrane protease IcsP to septa and new poles
The Shigella flexneri outer membrane (OM) protease IcsP (SopA) is a member of the enterobacterial Omptin family of proteases which cleaves the polarly localised OM protein IcsA that is essential for Shigella virulence. Unlike IcsA however, the specific localisation of IcsP on the cell surface is unknown. To determine the distribution of IcsP, a haemagglutinin (HA) epitope was inserted into the non-essential IcsP OM loop 5 using Splicing by Overlap Extension (SOE) PCR, and IcsP(HA) was characterised. Quantum Dot (QD) immunofluorescence (IF) surface labelling of IcsP(HA) was then undertaken. Quantitative fluorescence analysis of S. flexneri 2a 2457T treated with and without tunicaymcin to deplete lipopolysaccharide (LPS) O antigen (Oag) showed that IcsP(HA) was asymmetrically distributed on the surface of septating and non-septating cells, and that this distribution was masked by LPS Oag in untreated cells. Double QD IF labelling of IcsP(HA) and IcsA showed that IcsP(HA) preferentially localised to the new pole of non-septating cells and to the septum of septating cells. The localisation of IcsP(HA) in a rough LPS S. flexneri 2457T strain (with no Oag) was also investigated and a similar distribution of IcsP(HA) was observed. Complementation of the rough LPS strain with rmlD resulted in restored LPS Oag chain expression and loss of IcsP(HA) detection, providing further support for LPS Oag masking of surface proteins. Our data presents for the first time the distribution for the Omptin OM protease IcsP, relative to IcsA, and the effect of LPS Oag masking on its detection.Elizabeth Ngoc Hoa Tran, Matthew Thomas Doyle, Renato Moron
Evolution of the Aging Brain Transcriptome and Synaptic Regulation
Alzheimer's disease and other neurodegenerative disorders of aging are characterized by clinical and pathological features that are relatively specific to humans. To obtain greater insight into how brain aging has evolved, we compared age-related gene expression changes in the cortex of humans, rhesus macaques, and mice on a genome-wide scale. A small subset of gene expression changes are conserved in all three species, including robust age-dependent upregulation of the neuroprotective gene apolipoprotein D (APOD) and downregulation of the synaptic cAMP signaling gene calcium/calmodulin-dependent protein kinase IV (CAMK4). However, analysis of gene ontology and cell type localization shows that humans and rhesus macaques have diverged from mice due to a dramatic increase in age-dependent repression of neuronal genes. Many of these age-regulated neuronal genes are associated with synaptic function. Notably, genes associated with GABA-ergic inhibitory function are robustly age-downregulated in humans but not in mice at the level of both mRNA and protein. Gene downregulation was not associated with overall neuronal or synaptic loss. Thus, repression of neuronal gene expression is a prominent and recently evolved feature of brain aging in humans and rhesus macaques that may alter neural networks and contribute to age-related cognitive changes
- …