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We investigated the in silico characterization of short-length nucleotide sequences that were differentially expressed in dieback stress-induced transcriptomic analysis. They displayed homology with C-terminal flanking peptides and defensins-like proteins, revealing their antimicrobial activity. Their predicted fingerprints displayed protein signatures related to antimicrobial peptides. These short-length RGAs have been shown to possess structural motifs such as APLT P-type ATPase, casein kinase II (CK2), protein kinase 3, protein kinase C (PKC), and N-glycosylation site that are the attributes of disease resistance genes. The prediction of arginine and lysine residues in active binding sites in ligand docking analysis prophesied them as antimicrobial peptides due to their strong relation with antimicrobial activity. The in silico structural–functional characterization has predicted their role in resistance against microbial pathogens. Moreover, the predicted antimicrobial peptide regions showed their homology with the signature domain of PR-5-like protein and AMP family Thaumatin

Background: Overexpression of mucin-5AC (MUC5AC) makes it a targetable biomarker in pancreatic cancer. The present study evaluated tumor targeting with a MUC5AC antibody conjugated to a near-infrared dye in a patient-derived orthotopic xenograft (PDOX) mouse model. Materials and Methods: MUC5AC monoclonal antibody was conjugated to the near-infrared dye IRDye800CW to synthesize MUC5AC-IR800. PDOX models were established by implanting a high-MUC5AC-expressing patient-derived pancreatic tumor on the pancreas of nude mice. After 4 weeks of PDOX tumor growth, mice were imaged after receiving MUC5AC-IR800 (75 μg) intravenously. Results: In the PDOX models, MUC5AC-IR800 selectively and brightly targeted the pancreatic tumor (tumor to background ratio: 2.46±0.465). Conclusion: MUC5AC-IR800 provides distinct visualization of pancreatic tumors. MUC5AC-IR800 may be used clinically in the future to improve pancreatic cancer resection. This novel fluorescent probe is also promising for targeting of pre-malignant pancreatic lesions with subsequent resection under fluorescence guidance.

Fusarium oxysporum f. sp. apii race 4, which is in F. oxysporum species complex (FOSC) Clade 2, causes a new Fusarium wilt of celery. We compared F. oxysporum f. sp. apii race 4 with race 2, which causes Fusarium yellows of celery and is in FOSC Clade 3. Optimal temperatures for celery yield are 16 to 18°C. Soil temperatures in California celery production areas can range up to 26°C, and the maximal rate of hyphal extension of F. oxysporum f. sp. apii races 2 and 4 in culture are 25 and 28°C, respectively. Here, we compared the effect of temperatures from 16 to 26°C on growth of F. oxysporum f. sp. apii races 4 and 2 in two celery cultivars: Challenger, which is resistant to F. oxysporum f. sp. apii race 2 and susceptible to race 4; and Sonora, which is susceptible to both F. oxysporum f. sp. apii races 2 and 4. Based on linear regressions, as temperature increases, there is an increase in the log of F. oxysporum f. sp. apii race 4 DNA concentration in celery crowns and in the reduction in plant height. Based on logistic regressions, as temperature increases, the incidence of vascular discoloration increases in celery with either F. oxysporum f. sp. apii race 2 or 4 infection. In both cultivars, temperatures of 22°C and above resulted in a significantly (α = 0.05) greater concentration of F. oxysporum f. sp. apii race 4 than race 2 in planta. The concentration of F. oxysporum f. sp. apii race 2 in crowns in 'Challenger' is temperature-independent and comparatively low; consequently, 'Challenger' is, at least partly, resistant rather than tolerant to F. oxysporum f. sp. apii race 2.

El presente trabajo se centra en el estudio de algunos algoritmos que se engloban bajo el concepto de Machine Learning aplicados a la clasificación de textos, y hacer una comparativa entre ellos en cuanto a la eficacia y precisión a la hora de realizar las agrupaciones en cada uno de los casos. El primero de ellos consiste en la clasificación de los emails, si son spam o no, y el segundo se centra en la clasificación de las noticias en sus correspondientes categorías. Los algoritmos que se han elegido son el de Naive Bayes y el de Support Vector Machine. Tras el correspondiente análisis de los resultados se llegaron a varias conclusiones. Primero de todo, hay que destacar la necesidad e importancia de un correcto preprocesamiento de los datos. Si se lleva a cabo de una forma correcta y recomendable, las diferencias en los resultados finales son notables. Segundo, según el tipo de datos y de acuerdo con la forma de prepararlos, existen funciones que se pueden adaptar mejor al modelo que otras, y de esta forma influir de una manera directa sobre los resultados deseados. Por último, indicar que de entre los modelos que se emplearon para la resolución de los casos, aquel que mejor se adaptó y que realizó las clasificaciones con una mayor precisión fue el de Support Vector Machine.

Additional file 10 Conserved synteny of BUSCOs in Foa race 4 and other Foa, Foci and a reference

Additional file 2 Virulence of F. oxysporum f. sp. apii (Foa) races in three differential celery cultivars

Additional file 21 Percentage of the genome with transposons and repeats in Foa, Foci, and the Fol reference

Additional file 14 Foa race 4 putative accessory chromosomes: percentage of genes that have homologs in other strains

Additional file 4 Locations of the core genome in the Foa and Foci assemblies

Additional file 16 Up-expressed in planta RNA TagSeq-predicted effectors in Foa race 4: sequences, distribution, and mimp associations

Additional file 18 Test of PCR primers for Foa races 2 and 4 and Foci on a diversity of Fusarium spp.

Additional file 6 A cladogram of the mitochondrial genomes of the Foa, Foci, and 34 FOSC strains

Additional file 1. Isolate collection

Additional file 20 Diagnostic PCR primers for Foa race 2 haplogroup, Foa race 4, and Foci

Additional file 13 Synteny between the two Foci strains in the conserved and accessory genomes.

Additional file 7. The numbers of genes and the sizes of the core and accessory genomes

Additional file 5. Percentage of the 3725 Benchmarking Universal Single-Copy Orthologs (BUSCO) in Sordariomycetes in the sequenced strains

Additional file 12 Synteny between FociGL306 and Foa race 4 in the conserved and accessory genomes

Additional file 11. The number of homologs and their synteny in the accessory genomes

Additional file 9 Classification of contigs in the Foci3–2 accessory genome as either lineage- or host-specific

Additional file 19 Whole genome-sequenced Fusarium spp. included in analyses in GenBank wgs

Additional file 15 Homologs of gene models from Fol4287 chromosome 14 in Foa race 4 and FociGL306

Additional file 3 Virulence of F. oxysporum f. sp. apii and f. sp. coriandrii in celery and coriander

Dieback, or “dead arm,” in noncoastal California grapevines is most commonly caused by Botryosphaeria spp. Using Koch's postulates, we demonstrated that isolates of B. obtusa are pathogenic on grapevines. We initiated studies to investigate the life cycle of B. obtusa and ways to control it with cultural practices. Fungal spores disseminated by rainstorms were collected in traps in an Arbuckle vineyard from December 2006 through spring 2007. The data suggests that B. obtusa was rain-disseminated throughout winter and spring, and that pycnidia on deadwood in the vines is a major source of inoculum for new infections. Transmission may also be possible via vegetative propagation, pruning shears and insects. Durable latex paints were investigated for protecting pruning and surgical wounds; a self-priming latex paint was shown to be an effective barrier and was nonphytotoxic.

Additional file 1 : Figure S1. MUC5AC mediates colon cancer cell motility, migration, and invasion. (A) MUC5AC expression was up-regulated in human CRC cell lines (HCT-8 and LS174T) as compared to a normal colon cell line (CCD 841 CoN). A549 (lung cancer cell line) was used as a positive control. (B) Cell viability of HCT-8 and LS174T cell lines stably transfected with Scr and Sh5AC was assessed by MTT assay. (C) Colony formation assay showed fewer colonies in Sh5AC cell lines compared with Scr. (D) The presence of MUC5AC in Scr cell lines increased colon cancer migration (by Boyden chamber) and invasion (by matrigel coating). (E) Sh5AC cells exhibited less cell migration than Scr cells in the wound healing assay. Figure S2. Animals with orthotopic implantation of parental MUC5AC cell lines showed different metastatic lesions as compared to knockout group. Figure S3. MUC5AC knockout sensitizes colon cancer cells to 5-FU treatment. (A and B) Cell viability was measured by MTT assay. Bar diagram indicating 5-FU and oxaliplatin treatment for 48 h significantly decreased cell viability in KO clones (Clone-1 and -2) compared with parental HCT-8 and LS174T CRC cell lines.

Additional file 1 : Figure S1. MUC5AC mediates colon cancer cell motility, migration, and invasion. (A) MUC5AC expression was up-regulated in human CRC cell lines (HCT-8 and LS174T) as compared to a normal colon cell line (CCD 841 CoN). A549 (lung cancer cell line) was used as a positive control. (B) Cell viability of HCT-8 and LS174T cell lines stably transfected with Scr and Sh5AC was assessed by MTT assay. (C) Colony formation assay showed fewer colonies in Sh5AC cell lines compared with Scr. (D) The presence of MUC5AC in Scr cell lines increased colon cancer migration (by Boyden chamber) and invasion (by matrigel coating). (E) Sh5AC cells exhibited less cell migration than Scr cells in the wound healing assay. Figure S2. Animals with orthotopic implantation of parental MUC5AC cell lines showed different metastatic lesions as compared to knockout group. Figure S3. MUC5AC knockout sensitizes colon cancer cells to 5-FU treatment. (A and B) Cell viability was measured by MTT assay. Bar diagram indicating 5-FU and oxaliplatin treatment for 48 h significantly decreased cell viability in KO clones (Clone-1 and -2) compared with parental HCT-8 and LS174T CRC cell lines.