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BackgroundThere is a high rate of positive surgical margins with resection of liver metastases in colorectal cancer (CRC). The present study reports using a fluorescent anti-mucin 4 (MUC4) antibodies to label primary CRC and liver metastases to better visualize tumor margins in mouse models.MethodsWestern blotting for MUC4 protein expression of normal colon and CRC tumor lysates was performed. Orthotopic primary and liver metastatic CRC mouse models received anti-MUC4 antibody conjugated to IR800 (MUC4-IR800). Mice were sacrificed and imaged after 48 hours.ResultsWestern blotting demonstrated increased MUC4 expression in a human CRC cell line and patient-derived primary and liver-metastatic CRCs. The LS174T orthotopic primary CRC model tumor to background ratio (TBR) was 2.04 (±0.35). The patient-derived orthotopic xenograft (PDOX) primary CRC model TBR was 2.17 (±0.35). The PDOX liver metastasis model TBR was 1.56 (±0.53).ConclusionMUC4-IR800 provided bright labeling of primary and liver tumors in CRC orthotopic mouse models, demonstrating their future clinical potential for margin visualization in fluorescence guided surgery.

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.

BackgroundOverexpression 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 methodsMUC5AC 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.ResultsIn the PDOX models, MUC5AC-IR800 selectively and brightly targeted the pancreatic tumor (tumor to background ratio: 2.46±0.465).ConclusionMUC5AC-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 (Foa) race 4, which is in F. oxysporum species complex (FOSC) Clade 2, causes a new Fusarium wilt of celery. We compared Foa 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 Foa races 2 and 4 in culture are 25°C and 28°C, respectively. Here, we compared the effect of temperatures from 16 to 26°C on growth of Foa races 4 and 2 in two celery cultivars: Challenger, which is resistant to Foa race 2 and susceptible to race 4; and Sonora, which is susceptible to both Foa races 2 and 4. Based on linear regressions, as temperature increases, there is an increase in the log of Foa 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 Foa race 2 or 4 infection. In both cultivars, temperatures of 22°C and above resulted in a significantly (α=0.05) greater concentration of Foa race 4 than race 2 in planta. The concentration of Foa race 2 in crowns in Challenger is temperature-independent and comparatively low; consequently, Challenger is, at least partly, resistant rather than tolerant to Foa race 2.

To meet the requirements of California's Sustainable Groundwater Management Act, there is a critical need for crop production strategies with less reliance on irrigation from surface and groundwater sources. One strategy for improving agricultural water use efficiency is reducing tillage and maintaining residues on the soil surface. We evaluated high residue no-till versus standard tillage in the San Joaquin Valley with and without cover crops on the yields of two crops, garbanzo and sorghum, for 4 years. The no-till treatment had no primary or secondary tillage. Sorghum yields were similar in no-till and standard tillage systems while no-till garbanzo yields matched or exceeded those of standard tillage, depending on the year. Cover crops had no effect on crop yields. Soil cover was highest under the no-till with cover crop system, averaging 97% versus 5% for the standard tillage without cover crop system. Our results suggest that garbanzos and sorghum can be grown under no-till practices in the San Joaquin Valley without loss of yield.

BackgroundMembers of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.ResultsA phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.ConclusionsThere was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.

More virulent and aggressive races of Puccinia striiformis f. sp. tritici (Pst), the pathogen causing wheat stripe rust, have been spreading around the world since 2000 causing large grain yield losses. A better understanding of the genome and genetic diversity of these new Pst races will be useful to develop new strategies to ameliorate these losses. In this study, we generated an improved genome assembly of a post-2000 virulent race from the Western USA designated as PST-130. We implemented a haplotype phasing strategy using the diploid-aware assembler, Falcon-Unzip and new long-read technology from PacBio to phase the two genomes of this dikaryotic organism. The combination of these new technologies resulted in an improved PST-130 assembly with only 151 contigs (85.4 Mb, N50 of 1.44 Mb), and a complementary assembly (haplotigs) with 458 contigs (65.9 Mb, N50 of 0.235 Mb, PRJNA650506). This new assembly improved gene predictions resulting in 228 more predicted complete genes than in the initial Illumina assembly (29,178 contigs, N50 of 5 kb). The alignment of the non-repetitive primary and haplotig contigs revealed and average of 5.22 SNP/kb, with 39.1% showing 10 SNP/kb. This large divergent regions may represent introgressions of chromosome segments from more divergent Pst races in regions where a complete sexual cycle and recombination are possible. We hypothesize that some of the divergent regions in PST-130 may be related to the European "Warrior" race PST-DK0911 because this genome is more similar to PST-130 (3.18 SNP/kb) than to the older European race PST-104E (3.75 SNP/kb). Complete phasing of additional Pst genomes or sequencing individual nuclei will facilitate the tracing of the haploid genomes introduced by the new Pst races into local populations.

Fusarium oxysporum species complex (FOSC) isolates were obtained from celery with symptoms of Fusarium yellows between 1993 and 2013 primarily in California. Virulence tests and a two-gene dataset from 174 isolates indicated that virulent isolates collected before 2013 were a highly clonal population of F. oxysporum f. sp. apii race 2. In 2013, new highly virulent clonal isolates, designated race 4, were discovered in production fields in Camarillo, California. Long-read Illumina data were used to analyze 16 isolates: six race 2, one of each from races 1, 3, and 4, and seven genetically diverse FOSC that were isolated from symptomatic celery but are nonpathogenic on this host. Analyses of a 10-gene dataset comprising 38 kb indicated that F. oxysporum f. sp. apii is polyphyletic; race 2 is nested within clade 3, whereas the evolutionary origins of races 1, 3, and 4 are within clade 2. Based on 6,898 single nucleotide polymorphisms from the core FOSC genome, race 3 and the new highly virulent race 4 are highly similar with Nei's Da = 0.0019, suggesting that F. oxysporum f. sp. apii race 4 evolved from race 3. Next generation sequences were used to develop PCR primers that allow rapid diagnosis of races 2 and 4 in planta.

Ever since Stephen Paget's 1889 hypothesis, metastatic organotropism has remained one of cancer's greatest mysteries. Here we demonstrate that exosomes from mouse and human lung-, liver- and brain-tropic tumour cells fuse preferentially with resident cells at their predicted destination, namely lung fibroblasts and epithelial cells, liver Kupffer cells and brain endothelial cells. We show that tumour-derived exosomes uptaken by organ-specific cells prepare the pre-metastatic niche. Treatment with exosomes from lung-tropic models redirected the metastasis of bone-tropic tumour cells. Exosome proteomics revealed distinct integrin expression patterns, in which the exosomal integrins α6β4 and α6β1 were associated with lung metastasis, while exosomal integrin αvβ5 was linked to liver metastasis. Targeting the integrins α6β4 and αvβ5 decreased exosome uptake, as well as lung and liver metastasis, respectively. We demonstrate that exosome integrin uptake by resident cells activates Src phosphorylation and pro-inflammatory S100 gene expression. Finally, our clinical data indicate that exosomal integrins could be used to predict organ-specific metastasis.

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.

While walnut trees on Juglans hindsii x J. regia ‘Paradox’ rootstocks are highly susceptible to crown gall, it is unknown whether this bacterial disease is acquired in the nursery or the orchard. We selected two groups of gall-free trees in nurseries, those adjacent to trees with and without galls. Two years after being transplanted in the orchard, trees in the group adjacent to those with galls had significantly greater — more than four times more — crown gall incidence than those adjacent to trees without galls (14% versus 3%). In addition, trees in prolonged (17-day), bare-root, unrefrigerated storage before transplanting were associated with higher crown-gall incidence. We also found that crown gall can decrease walnut tree productivity. For every quarter of trunk circumference that was galled, there was a 12% decrease in cumulative nut yield over the first 4 years of production.