941 research outputs found
Further characterization of complex chromosomal rearrangements in myeloid malignancies: spectral karyotyping adds precision in defining abnormalities associated with poor prognosis
The mixed lineage leukemia gene (MLL, also known as HRX, ALL-1 and Htrx) located at 11q23 is involved in translocations with over 40 different chromosomal bands in a variety of leukemia subtypes. Here we report our analysis of a rare but recurring translocation, t(11;15)(q23;q14). This translocation has been described in a small subset of cases with both acute myeloblastic leukemia and ALL. Recent studies have shown that MLL is fused to AF15q14 in the t(11;15). Here we analyse a sample from another patient with this translocation and confirm the presence of an MLL-AF15q14 fusion. However, we have also identified and cloned another fusion transcript from the same patient sample. In this fusion transcript, MLL is fused to a novel gene, MLL partner containing FYVE domain (MPFYVE). Both MLL-AF15q14 and MLL-MPFYVE are in-frame fusion transcripts with the potential to code for novel fusion proteins. MPFYVE is also located on chromosome 15, approximately 170 kb telomeric to AF15q14. MPFYVE contains a highly conserved motif, the FYVE domain which, in other proteins, has been shown to bind to phosphotidyl-inositol-3 phosphate (PtdIns(3)P). The MLL-MPFYVE fusion may be functionally important in the leukemia process in at least some patients containing this translocation
Parity violation in nuclear systems
Parity violation in nuclear systems is reviewed. A few ingredients relevant
to the description of the parity-violating nucleon-nucleon force in terms of
meson exchanges are reminded. Effects in nuclear systems are then considered.
They involve pp scattering, some complex nuclei and the deuteron system.Comment: 4 pages, to be published in the proceedings of the worksho
Derivation of the effective action of a dilute Fermi gas in the unitary limit of the BCS-BEC crossover
The effective action describing the gapless Nambu-Goldstone, or
Anderson-Bogoliubov, mode of a zero-temperature dilute Fermi gas at unitarity
is derived up to next-to-leading order in derivatives from the microscopic
theory. Apart from a next-to-leading order term that is suppressed in the BCS
limit, the effective action obtained in the strong-coupling unitary limit is
proportional to that in the weak-coupling BCS limit.Comment: 13 pages, no figures; v2: discussion of one-dimensional system and
references adde
Molecular cytogenetic characterization of breakpoints in 19 patients with hematologic malignancies and 12p unbalanced translocations
Structural rearrangements of the short arm of chromosome 12 are frequent cytogenetic findings in various hematologic malignancies. The ETV6 gene is the most common target for rearrangements in 12p13. Fluorescence in situ hybridization (FISH) investigations have shown that translocations of 12p other than t(12;21) are frequently accompanied by small interstitial deletions that include ETV6. Unbalanced translocations involving ETV6 have rarely been described, and breakpoints outside ETV6 appear to be strongly associated with complex karyotypes. We studied bone marrow samples from 19 patients known to have 12p unbalanced translocations and complex karyotypes, using FISH and spectral karyotyping. FISH analysis confirmed the hemizygous deletion of the ETV6 and CDKN1B genes in 74% of cases. We found four cases with interstitial deletions. In these four cases and in two others (6/19, 31.5%), the fusion with the partner chromosome was in the subtelomeric region of 12p13.3, confirming that there is a recurrent breakpoint in this region
Spring-block model for a single-lane highway traffic
A simple one-dimensional spring-block chain with asymmetric interactions is
considered to model an idealized single-lane highway traffic. The main elements
of the system are blocks (modeling cars), springs with unidirectional
interactions (modeling distance keeping interactions between neighbors), static
and kinetic friction (modeling inertia of drivers and cars) and spatiotemporal
disorder in the values of these friction forces (modeling differences in the
driving attitudes). The traveling chain of cars correspond to the dragged
spring-block system. Our statistical analysis for the spring-block chain
predicts a non-trivial and rich complex behavior. As a function of the disorder
level in the system a dynamic phase-transition is observed. For low disorder
levels uncorrelated slidings of blocks are revealed while for high disorder
levels correlated avalanches dominates.Comment: 6 pages, 7 figure
-- mixing and oblique corrections in an model
A global fit for experiments is included in this revised version.Comment: IFP-460-UNC, TRI-PP-93-11, 20 pages, 2 figures are appende
Identification of new translocations involving ETV6 in hematologic malignancies by fluorescence in situ hybridization and spectral karyotyping
TEL/ETV6 is the first transcription factor identified that is specifically required for hematopoiesis within the bone marrow. This gene has been found to have multiple fusion partners; 35 different chromosome bands have been involved in ETV6 translocations, of which 13 have been cloned. To identify additional ETV6 partner genes and to characterize the chromosomal abnormalities more fully, we studied bone marrow samples from patients known to have rearrangements of 12p, using fluorescence in situ hybridization (FISH) and spectral karyotyping (SKY). FISH analysis was done with 14 probes located on 12p12.1 to 12p13.3. Nine ETV6 rearrangements were identified using FISH. The aberrations include t(1;12)(p36;p13), t(4;12)(q12;p13) (two patients), t(4;12)(q22;p13), t(6;12)(p21;p13), der(6)t(6;21)(q15;q?)t(12;21)(p13;q22), t(6;12)(q25;p13), inv(12)(p13q24), and t(2;2;5;12;17)(p25;q23;q31;p13;q12). Six new ETV6 partner bands were identified: 1p36, 4q22, 6p21, 6q25, 12q24, and 17q12. Our present data as well previous data from us and from other researchers suggest that ETV6 is involved in 41 translocations. The breakpoints in ETV6 were upstream from the exons coding for the HLH (helix-loop-helix) domain in six cases. Although cytogenetic analysis identified 12p abnormalities in all cases, FISH and SKY detected new and unexpected chromosomal rearrangements in many of them. Thus, complete characterization of the samples was achieved by using all three techniques in combination
Pairing of fermions in atomic traps and nuclei
Pairing gaps for fermionic atoms in harmonic oscillator traps are calculated
for a wide range of interaction strengths and particle number, and compared to
pairing in nuclei. Especially systems, where the pairing gap exceeds the level
spacing but is smaller than the shell splitting , are studied
which applies to most trapped Fermi atomic systems as well as to finite nuclei.
When solving the gap equation for a large trap with such multi-level pairing,
one finds that the matrix elements between nearby harmonic oscillator levels
and the quasi-particle energies lead to a double logarithm of the gap, and a
pronounced shell structure at magic numbers. It is argued that neutron and
proton pairing in nuclei belongs to the class of multi-level pairing, that
their shell structure follows naturally and that the gaps scale as - all in qualitative agreement with odd-even staggering of nuclear
binding energies. Pairing in large systems are related to that in the bulk
limit. For large nuclei the neutron and proton superfluid gaps approach the
asymptotic value in infinite nuclear matter: MeV.Comment: 11 pages, 5 figure
Resonance effects on the crossover of bosonic to fermionic superfluidity
Feshbach scattering resonances are being utilized in atomic gases to explore
the entire crossover region from a Bose-Einstein Condensation (BEC) of
composite bosons to a Bardeen-Cooper-Schrieffer (BCS) of Cooper pairs. Several
theoretical descriptions of the crossover have been developed based on an
assumption that the fermionic interactions are dependent only on the value of a
single microscopic parameter, the scattering length for the interaction of
fermion particles. Such a picture is not universal, however, and is only
applicable to describe a system with an energetically broad Feshbach resonance.
In the more general case in which narrow Feshbach resonances are included in
the discussion, one must consider how the energy dependence of the scattering
phase shift affects the physical properties of the system. We develop a
theoretical framework which allows for a tuning of the scattering phase shift
and its energy dependence, whose parameters can be fixed from realistic
scattering solutions of the atomic physics. We show that BCS-like nonlocal
solutions may build up in conditions of resonance scattering, depending on the
effective range of the interactions.Comment: 8 pages,7 figure
Genome And Secretome Analysis Of The Hemibiotrophic Fungal Pathogen, Moniliophthora Roreri, Which Causes Frosty Pod Rot Disease Of Cacao: Mechanisms Of The Biotrophic And Necrotrophic Phases
Background: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.Results: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.Conclusions: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. © 2014 Meinhardt et al.; licensee BioMed Central Ltd.151USDA; U.S. Department of AgricultureLatunde-Dada, A.O., Colletotrichum: tales of forcible entry, stealth, transient confinement and breakout (2001) Mol Plant Pathol, 2 (4), pp. 187-198. , 10.1046/j.1464-6722.2001.00069.x, 20573006Oliver, R.P., Ipcho, S.V.S., Arabidopsis pathology breathes new life into the necrotrophs-vs.-biotrophs classification of fungal pathogens (2004) Mol Plant Pathol, 5 (4), pp. 347-352. , 10.1111/j.1364-3703.2004.00228.x, 20565602Catanzariti, A.M., Dodds, P.N., Lawrence, G.J., Ayliffe, M.A., Ellis, J.G., Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors (2006) Plant Cell, 18 (1), pp. 243-256. , 10.1105/tpc.105.035980, 1323496, 16326930Link, T.I., Voegele, R.T., Secreted proteins of Uromyces fabae: similarities and stage specificity (2008) Mol Plant Pathol, 9 (1), pp. 59-66Brown, N.A., Antoniw, J., Hammond-Kosack, K.E., The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis (2012) Plos One, 7 (4), pp. e33731. , 10.1371/journal.pone.0033731, 3320895, 22493673Thomma, B.P., Alternaria spp.: from general saprophyte to specific parasite (2003) Mol Plant Pathol, 4 (4), pp. 225-236. , 10.1046/j.1364-3703.2003.00173.x, 20569383Evans, H.C., Stalpers, J.A., Samson, R.A., Benny, G.L., Taxonomy of Monilia-Roreri, an important pathogen of theobroma-cacao in South-America (1978) Can J Bot, 56 (20), pp. 2528-2532Aime, M.C., Phillips-Mora, W., The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae (2005) Mycologia, 97 (5), pp. 1012-1022. , 10.3852/mycologia.97.5.1012, 16596953Phillips-Mora, W., Wilkinson, M.J., Frosty pod of cacao: a disease with a limited geographic range but unlimited potential for damage (2007) Phytopathology, 97 (12), pp. 1644-1647. , 10.1094/PHYTO-97-12-1644, 18943726Meinhardt, L.W., Rincones, J., Bailey, B.A., Aime, M.C., Griffith, G.W., Zhang, D.P., Pereira, G.A.G., Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe? (2008) Mol Plant Pathol, 9 (5), pp. 577-588. , 10.1111/j.1364-3703.2008.00496.x, 19018989Ferreira, L.F.R., Duarte, K.M.R., Gomes, L.H., Carvalho, R.S., Leal, G.A., Aguiar, M.M., Armas, R.D., Tavares, F.C.A., Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae) (2012) Genet Mol Res, 11 (3), pp. 2559-2568. , 10.4238/2012.July.10.11, 22869076Phillips-Mora, W., Wilkinson, M.J., Frosty pod: a disease of limited geographic distribution but unlimited potential for damage (2006) Phytopathology, 96 (6), pp. S138-S138Evans, H.C., (1981) Pod Rot of Cacao caused by Moniliophthora (Monilia) roreri, , London: Commonwealth Agricultural Bureau, 24Joosten, M., de Wit, P., THE TOMATO-CLADOSPORIUM FULVUM INTERACTION: a versatile experimental system to study plant-pathogen interactions (1999) Annu Rev Phytopathol, 37, pp. 335-367. , 10.1146/annurev.phyto.37.1.335, 11701827Perfect, S.E., Green, J.R., Infection structures of biotrophic and hemibiotrophic fungal plant pathogens (2001) Mol Plant Pathol, 2 (2), pp. 101-108. , 10.1046/j.1364-3703.2001.00055.x, 20572997Scarpari, L.M., Meinhardt, L.W., Mazzafera, P., Pomella, A.W.V., Schiavinato, M.A., Cascardo, J.C.M., Pereira, G.A.G., Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa (2005) J Exp Bot, 56 (413), pp. 865-877. , 10.1093/jxb/eri079, 15642708Melnick, R.L., Marelli, J., Bailey, B.A., The molecular interaction of Theobroma cacao and Moniliophthora perniciosa, causal agent of witches' broom, during infection of young pods (2011) Phytopathology, 101 (6), pp. S274-S274Melnick, R.L., Marelli, J.P., Sicher, R.C., Strem, M.D., Bailey, B.A., The interaction of Theobroma cacao and Moniliophthora perniciosa, the causal agent of witches' broom disease, during parthenocarpy (2012) Tree Genet Genomes, 8 (6), pp. 1261-1279Thomazella, D.P., Teixeira, P.J., Oliveira, H.C., Saviani, E.E., Rincones, J., Toni, I.M., Reis, O., Pereira, G.A., The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development (2012) New Phytol, 194 (4), pp. 1025-1034. , 10.1111/j.1469-8137.2012.04119.x, 3415677, 22443281Mondego, J.M., Carazzolle, M.F., Costa, G.G., Formighieri, E.F., Parizzi, L.P., Rincones, J., Cotomacci, C., Pereira, G.A.G., A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom disease of cacao (2008) Bmc Genomics, 9, p. 548. , 10.1186/1471-2164-9-548, 2644716, 19019209Bailey, B.A., Crozier, J., Sicher, R.C., Strem, M.D., Melnick, R., Carazzolle, M.F., Costa, G.G.L., Meinhardt, L., Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri (2013) Physiol Mol Plant P, 81, pp. 84-96Henrissat, B., A classification of glycosyl hydrolases based on amino acid sequence similarities (1991) Biochem J, 280 (PART 2), pp. 309-316. , 1130547, 1747104Dias, F.M., Vincent, F., Pell, G., Prates, J.A., Centeno, M.S., Tailford, L.E., Ferreira, L.M., Gilbert, H.J., Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A (2004) J Biol Chem, 279 (24), pp. 25517-25526. , 10.1074/jbc.M401647200, 15014076Fibriansah, G., Masuda, S., Koizumi, N., Nakamura, S., Kumasaka, T., The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 (2007) Proteins, 69 (3), pp. 683-690. , 10.1002/prot.21589, 17879342Markovic, O., Janecek, S., Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution (2001) Protein Eng, 14 (9), pp. 615-631. , 10.1093/protein/14.9.615, 11707607Vandermarliere, E., Bourgois, T.M., Winn, M.D., van Campenhout, S., Volckaert, G., Delcour, J.A., Strelkov, S.V., Courtin, C.M., Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family (2009) Biochem J, 418 (1), pp. 39-47. , 10.1042/BJ20081256, 18980579Tiels, P., Baranova, E., Piens, K., De Visscher, C., Pynaert, G., Nerinckx, W., Stout, J., Callewaert, N., A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes (2012) Nat Biotechnol, 30 (12), pp. 1225-1231. , 10.1038/nbt.2427, 23159880Ferreira, P., Hernandez-Ortega, A., Herguedas, B., Martinez, A.T., Medina, M., Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates (2009) J Biol Chem, 284 (37), pp. 24840-24847. , 10.1074/jbc.M109.011593, 2757187, 19574215Mayer, A.M., Staples, R.C., Laccase: new functions for an old enzyme (2002) Phytochemistry, 60 (6), pp. 551-565. , 10.1016/S0031-9422(02)00171-1, 12126701Kersten, P.J., Glyoxal oxidase of Phanerochaete chrysosporium: its characterization and activation by lignin peroxidase (1990) Proc Natl Acad Sci U S A, 87 (8), pp. 2936-2940. , 10.1073/pnas.87.8.2936, 53808, 11607073Henrissat, B., Callebaut, I., Fabrega, S., Lehn, P., Mornon, J.P., Davies, G., Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases (1995) Proc Natl Acad Sci U S A, 92 (15), pp. 7090-7094. , 10.1073/pnas.92.15.7090, 41477, 7624375Wostemeyer, J., Kreibich, A., Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution (2002) Curr Genet, 41 (4), pp. 189-198. , 10.1007/s00294-002-0306-y, 12172959Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Oliver, S.G., Life with 6000 genes (1996) Science, 274 (5287), pp. 546-563. , 547, 10.1126/science.274.5287.546, 8849441Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Nicol, R., The genome sequence of the rice blast fungus Magnaporthe grisea (2005) Nature, 434 (7036), pp. 980-986. , 10.1038/nature03449, 15846337Labbe, J., Murat, C., Morin, E., Tuskan, G.A., Le Tacon, F., Martin, F., Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor (2012) Plos One, 7 (8), pp. e40197. , 10.1371/journal.pone.0040197, 3411680, 22870194Adomako, D., Cocoa pod husk pectin (1972) Phytochemistry, 11 (3), p. 1145Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R.J., Narusaka, Y., Takano, Y., Shirasu, K., Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi (2013) New Phytol, 197 (4), pp. 1236-1249. , 10.1111/nph.12085, 23252678Garcia, O., Macedo, J.A.N., Tiburcio, R., Zaparoli, G., Rincones, J., Bittencourt, L.M.C., Ceita, G.O., Cascardo, J.C., Characterization of necrosis and ethylene-inducing proteins (NEP) in the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom in Theobroma cacao (2007) Mycol Res, 111, pp. 443-455. , 10.1016/j.mycres.2007.01.017, 17512713Pemberton, C.L., Salmond, G.P., The Nep1-like proteins-a growing family of microbial elicitors of plant necrosis (2004) Mol Plant Pathol, 5 (4), pp. 353-359. , 10.1111/j.1364-3703.2004.00235.x, 20565603Zaparoli, G., Barsottini, M.R., de Oliveira, J.F., Dyszy, F., Teixeira, P.J., Barau, J.G., Garcia, O., Dias, S.M., The crystal structure of necrosis-and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity (2011) Biochemistry-Us, 50 (45), pp. 9901-9910Cabral, A., Oome, S., Sander, N., Kufner, I., Nurnberger, T., Van den Ackerveken, G., Nontoxic Nep1-like proteins of the downy mildew pathogen Hyaloperonospora arabidopsidis: repression of necrosis-inducing activity by a surface-exposed region (2012) Mol Plant Microbe Interact, 25 (5), pp. 697-708. , 10.1094/MPMI-10-11-0269, 22235872Mosquera, G., Giraldo, M.C., Khang, C.H., Coughlan, S., Valent, B., Interaction transcriptome analysis identifies magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease (2009) Plant Cell, 21 (4), pp. 1273-1290. , 10.1105/tpc.107.055228, 2685627, 19357089Paper, J.M., Scott-Craig, J.S., Adhikari, N.D., Cuomo, C.A., Walton, J.D., Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum (2007) Proteomics, 7 (17), pp. 3171-3183. , 10.1002/pmic.200700184, 17676664van den Burg, H.A., Harrison, S.J., Joosten, M.H., Vervoort, J., de Wit, P.J., Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection (2006) Mol Plant Microbe Interact, 19 (12), pp. 1420-1430. , 10.1094/MPMI-19-1420, 17153926Roby, D., Gadelle, A., Toppan, A., Chitin oligosaccharides as elicitors of chitinase activity in melon plants (1987) Biochem Biophys Res Commun, 143 (3), pp. 885-892. , 10.1016/0006-291X(87)90332-9, 3566760Deising, H., Siegrist, J., Chitin deacetylase activity of the rust uromyces-viciae-fabae is controlled by fungal morphogenesis (1995) Fems Microbiol Lett, 127 (3), pp. 207-211Teixeira, P.J.P.L., Thomazella, D.P.T., Vidal, R.O., Do Prado, P.F.V., Reis, O., Baroni, R.M., Franco, S.F., Mondego, J.M.C., The fungal pathogen moniliophthora perniciosa has genes similar to plant PR-1 that are highly expressed during its interaction with cacao (2012) Plos One, 7 (9)Riviere, M.P., Marais, A., Ponchet, M., Willats, W., Galiana, E., Silencing of acidic pathogenesis-related PR-1 genes increases extracellular beta-(1→ 3)-glucanase activity at the onset of tobacco defence reactions (2008) J Exp Bot, 59 (6), pp. 1225-1239. , 10.1093/jxb/ern044, 18390849Levy, A., Guenoune-Gelbart, D., Epel, B.L., Beta-1,3-Glucanases: plasmodesmal gate keepers for intercellular communication (2007) Plant Signal Behav, 2 (5), pp. 404-407. , 10.4161/psb.2.5.4334, 2634228, 19704615Prados-Rosales, R.C., Roldan-Rodriguez, R., Serena, C., Lopez-Berges, M.S., Guarro, J., Martinez-del-Pozo, A., Di Pietro, A., A PR-1-like protein of fusarium oxysporum functions in virulence on mammalian hosts (2012) J Biol Chem, 287 (26), pp. 21970-21979. , 10.1074/jbc.M112.364034, 3381157, 22553200Kershaw, M.J., Talbot, N.J., Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis (1998) Fungal Genet Biol, 23 (1), pp. 18-33. , 10.1006/fgbi.1997.1022, 9501475Zelena, K., Takenberg, M., Lunkenbein, S., Woche, S.K., Nimtz, M., Berger, R.G., PfaH2: a novel hydrophobin from the ascomycete Paecilomyces farinosus (2013) Biotechnol Appl Biochem, 60 (2), pp. 147-154. , 10.1002/bab.1077, 23600571Wosten, H.A., Hydrophobins: multipurpose proteins (2001) Annu Rev Microbiol, 55, pp. 625-646. , 10.1146/annurev.micro.55.1.625, 11544369Bayry, J., Aimanianda, V., Guijarro, J.I., Sunde, M., Latge, J.P., Hydrophobins-unique fungal proteins (2012) PLoS Pathog, 8 (5), pp. e1002700. , 10.1371/journal.ppat.1002700, 3364958, 22693445De Oliveira, A.L., Gallo, M., Pazzagli, L., Benedetti, C.E., Cappugi, G., Scala, A., Pantera, B., Cicero, D.O., The structure of the elicitor cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double psi beta-barrel fold and carbohydrate binding (2011) J Biol Chem, 286 (20), pp. 17560-17568. , 10.1074/jbc.M111.223644, 3093830, 21454637Baccelli, I., Comparini, C., Bettini, P.P., Martellini, F., Ruocco, M., Pazzagli, L., Bernardi, R., Scala, A., The expression of the cerato-platanin gene is related to hyphal growth and chlamydospores formation in Ceratocystis platani (2012) Fems Microbiol Lett, 327 (2), pp. 155-163. , 10.1111/j.1574-6968.2011.02475.x, 22136757Zaparoli, G., Cabrera, O.G., Medrano, F.J., Tiburcio, R., Lacerda, G., Pereira, G.G., Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins (2009) Mycol Res, 113, pp. 61-72. , 10.1016/j.mycres.2008.08.004, 18796332Lombardi, L., Faoro, F., Luti, S., Baccelli, I., Martellini, F., Bernardi, R., Picciarelli, P., Pazzagli, L., Differential timing of defense-related responses induced by cerato-platanin and cerato-populin, two non-catalytic fungal elicitors (2013) Physiol Plant, 149, pp. 408-421Yang, Y., Zhang, H., Li, G., Li, W., Wang, X., Song, F., Ectopic expression of MgSM1, a Cerato-platanin family protein from Magnaporthe grisea, confers broad-spectrum disease resistance in Arabidopsis (2009) Plant Biotechnol J, 7 (8), pp. 763-777. , 10.1111/j.1467-7652.2009.00442.x, 19754836Bhadauria, V., Banniza, S., Vandenberg, A., Selvaraj, G., Wei, Y., EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum (2011) Bmc Genomics, 12, p. 327. , 10.1186/1471-2164-12-327, 3149586, 21699715Frischmann, A., Neudl, S., Gaderer, R., Bonazza, K., Zach, S., Gruber, S., Spadiut, O., Seidl-Seiboth, V., Self-assembly at air/water interfaces and carbohydrate binding properties of the small secreted protein EPL1 from the fungus trichoderma atroviride (2013) J Biol Chem, 288 (6), pp. 4278-4287. , 10.1074/jbc.M112.427633, 3567679, 23250741Jeong, J.S., Mitchell, T.K., Dean, R.A., The magnaporthe grisea snodprot1 homolog, MSP1, is required for virulence (2007) Fems Microbiol Lett, 273 (2), pp. 157-165. , 10.1111/j.1574-6968.2007.00796.x, 17590228Peter, M., Courty, P.E., Kohler, A., Delaruelle, C., Martin, D., Tagu, D., Frey-Klett, P., Martin, F., Analysis of expressed sequence tags from the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus (2003) New Phytol, 159 (1), pp. 117-129Cosgrove, D.J., Loosening of plant cell walls by expansins (2000) Nature, 407 (6802), pp. 321-326. , 10.1038/35030000, 11014181Quiroz-Castaneda, R.E., Martinez-Anaya, C., Cuervo-Soto, L.I., Segovia, L., Folch-Mallol, J.L., Loosenin, a novel protein with cellulose-disrupting activity from Bjerkandera adusta (2011) Microb Cell Fact, 10, p. 8. , 10.1186/1475-2859-10-8, 3050684, 21314954Brotman, Y., Briff, E., Viterbo, A., Chet, I., Role of swollenin, an expansin-like protein from Trichoderma, in plant root colonization (2008) Plant Physiol, 147 (2), pp. 779-789. , 10.1104/pp.108.116293, 2409044, 18400936Yamada, M., Sakuraba, S., Shibata, K., Taguchi, G., Inatomi, S., Okazaki, M., Shimosaka, M., Isolation and analysis of genes specifically expressed during fruiting body development in the basidiomycete Flammulina velutipes by fluorescence differential display (2006) Fems Microbiol Lett, 254 (1), pp. 165-172. , 10.1111/j.1574-6968.2005.00023.x, 16451195Rincones, J., Scarpari, L.M., Carazzolle, M.F., Mondego, J.M.C., Formighieri, E.F., Barau, J.G., Costa, G.G.L., Pereira, G.A., Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa (2008) Mol Plant Microbe In, 21 (7), pp. 891-908Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs (2008) Genome Res, 18 (5), pp. 821-829. , 10.1101/gr.074492.107, 2336801, 18349386Sommer, D.D., Delcher, A.L., Salzberg, S.L., Pop, M., Minimus: a fast, lightweight genome assembler (2007) BMC Bioinforma, 8, p. 64Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training (2008) Genome Res, 18 (12), pp. 1979-1990. , 10.1101/gr.081612.108, 2593577, 18757608Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., Morgenstern, B., AUGUSTUS: ab initio prediction of alternative transcripts (2006) Nucleic Acids Res, 34, pp. W435-W439. , Web Server issue, 1538822, 16845043Stanke, M., Tzvetkova, A., Morgenstern, B., AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome (2006) Genome Biol, 7 (SUPPL. 1), pp. S11 11-18Slater, G.S., Birney, E., Automated generation of heuristics for biological sequence comparison (2005) BMC Bioinforma, 6, p. 31Borodovsky, M., Lomsadze, A., Ivanov, N., Mills, R., Eukaryotic gene prediction using GeneMark.hmm (2003) Curr Protoc Bioinformatics, , Chapter 4, Unit4 6Haas, 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 (1), pp. R7. , 10.1186/gb-2008-9-1-r7, 2395244, 18190707Koski, L.B., Gray, M.W., Lang, B.F., Burger, G., AutoFACT: an automatic functional annotation and classification tool (2005) BMC Bioinforma, 6, p. 151Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., Wu, C.H., UniRef: comprehensive and non-redundant UniProt reference clusters (2007) Bioinformatics, 23 (10), pp. 1282-1288. , 10.1093/bioinformatics/btm098, 17379688Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Sonnhammer, E.L., The Pfam protein families database (2002) Nucleic Acids Res, 30 (1), pp. 276-280. , 10.1093/nar/30.1.276, 99071,
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