Measuring the Pharmacodynamic Effects of a Novel Hsp90 Inhibitor on HER2/neu Expression in Mice Using 89Zr-DFO-Trastuzumab

The positron-emitting radionuclide (89)Zr (t(1/2) = 3.17 days) was used to prepare (89)Zr-radiolabeled trastuzumab for use as a radiotracer for characterizing HER2/neu-positive breast tumors. In addition, pharmacodynamic studies on HER2/neu expression levels in response to therapeutic doses of PU-H71 (a specific inhibitor of heat-shock protein 90 [Hsp90]) were conducted.Trastuzumab was functionalized with desferrioxamine B (DFO) and radiolabeled with [(89)Zr]Zr-oxalate at room temperature using modified literature methods. ImmunoPET and biodistribution experiments in female, athymic nu/nu mice bearing sub-cutaneous BT-474 (HER2/neu positive) and/or MDA-MB-468 (HER2/neu negative) tumor xenografts were conducted. The change in (89)Zr-DFO-trastuzumab tissue uptake in response to high- and low-specific-activity formulations and co-administration of PU-H71 was evaluated by biodistribution studies, Western blot analysis and immunoPET. (89)Zr-DFO-trastuzumab radiolabeling proceeded in high radiochemical yield and specific-activity 104.3+/-2.1 MBq/mg (2.82+/-0.05 mCi/mg of mAb). In vitro assays demonstrated >99% radiochemical purity with an immunoreactive fraction of 0.87+/-0.07. In vivo biodistribution experiments revealed high specific BT-474 uptake after 24, 48 and 72 h (64.68+/-13.06%ID/g; 71.71+/-10.35%ID/g and 85.18+/-11.10%ID/g, respectively) with retention of activity for over 120 h. Pre-treatment with PU-H71 was followed by biodistribution studies and immunoPET of (89)Zr-DFO-trastuzumab. Expression levels of HER2/neu were modulated during the first 24 and 48 h post-administration (29.75+/-4.43%ID/g and 41.42+/-3.64%ID/g, respectively). By 72 h radiotracer uptake (73.64+/-12.17%ID/g) and Western blot analysis demonstrated that HER2/neu expression recovered to baseline levels.The results indicate that (89)Zr-DFO-trastuzumab provides quantitative and highly-specific delineation of HER2/neu positive tumors, and has potential to be used to measure the efficacy of long-term treatment with Hsp90 inhibitors, like PU-H71, which display extended pharmacodynamic profiles

Disordered enthalpy–entropy descriptor for high-entropy ceramics discovery

The need for improved functionalities in extreme environments is fuelling interest in high-entropy ceramics1,2,3. Except for the computational discovery of high-entropy carbides, performed with the entropy-forming-ability descriptor4, most innovation has been slowly driven by experimental means1,2,3. Hence, advancement in the field needs more theoretical contributions. Here we introduce disordered enthalpy–entropy descriptor (DEED), a descriptor that captures the balance between entropy gains and enthalpy costs, allowing the correct classification of functional synthesizability of multicomponent ceramics, regardless of chemistry and structure. To make our calculations possible, we have developed a convolutional algorithm that drastically reduces computational resources. Moreover, DEED guides the experimental discovery of new single-phase high-entropy carbonitrides and borides. This work, integrated into the AFLOW computational ecosystem, provides an array of potential new candidates, ripe for experimental discoveries

Phenotypic and Genetic Studies of Grapevine

Plant breeding is the science of altering a plant's genetics to attain a desired phenotype. In this dissertation, I explore what phenotypes to measure when breeding for downy mildew resistance and improved floral scent and how to measure these phenotypes accurately and efficiently. Traditionally, downy mildew resistance has been measured by visually rating sporulation and hypersensitive response on leaves or leaf discs. However, such manual ratings become intractable when dealing with thousands of samples. Therefore, to measure sporulation on leaf discs, I developed a computer vision system that reduced phenotyping time by more than 90% when compared to manual ratings, and also was found to work well for phenotyping leaf trichomes. If phenotypes are collected in the vineyard, spatial variation from inoculum, soil, and microclimate might have an effect on these phenotypes. Testing this assumption, spatial processes explained some variance in vineyard phenotypes, but accounting for the spatial variance might not lead to significantly more accurate phenotypes. Quantitative phenotyping of floral scent for large numbers of grapevines using headspace analysis is not economically feasible, so I evaluated the robustness of a hexane extraction followed by gas chromatography-mass spectrometry to identify floral volatiles and found that it was robust regardless of extraction time when flowers were sampled from the same inflorescence. After obtaining phenotypes and genotypes of vines, quantitative trait loci are found, traditionally using one phenotype at a time. In our case, understanding how sporulation, HR, and leaf trichomes affected each other was of interest, in addition to how genetic markers affected the phenotypes, so I used Bayesian networks to explore these interactions. In one of two F1 families studied, HR had a positive effect on sporulation, and leaf trichomes had a negative effect on both HR and sporulation, suggesting that leaf trichome density can be selected for in breeding for downy mildew disease resistance. A breeding project was started with the intention of creating a dwarf grapevine with an attractive floral scent. With a complementary interest to understand what volatile compounds were responsible for the various floral scents in grapevine, a diverse set of genotypes from various Vitis spp. were phenotyped for floral scent and volatiles, and it was found that similar scents were generated from different sesquiterpene profiles. Overall, this dissertation spans key concepts in the science of plant breeding, from parental selection and hybridization, to phenotyping by computer vision and chemical analysis, to statistical analyses of interacting phenotypes, genotypes, and spatial variability, with the findings possibly enhancing grapevine breeding strategies and execution

Additional file 1 of Genome-wide allele frequency studies in Pacific oyster families identify candidate genes for tolerance to ostreid herpesvirus 1 (OsHV-1)

Additional file 1: Fig. S1. Pedigree of families 30.004, 30.058, 30.062, and 30.065. Ancestry prior to cohort 22 is not shown as families in these cohorts were not spawned using single pair matings

Understanding the pharmacological properties of a metabolic PET tracer in prostate cancer

Generally, solid tumors (\u3e400 mm3) are inherently acidic, with more aggressive growth producing greater acidity. If the acidity could be targeted as a biomarker, it would provide a means to gauge the pace of tumor growth and degree of invasiveness, as well as providing a basis for predicting responses to pH-dependent chemotherapies. We have developed a 64Cu pH (low) insertion peptide (pHLIP) for targeting, imaging, and quantifying acidic tumors by PET, and our findings reveal utility in assessing prostate tumors. The new pHLIP version limits indiscriminate healthy tissue binding, and we demonstrate its targeting of extracellular acidification in three different prostate cancer models, each with different vascularization and acid-extruding protein carbonic anhydrase IX (CAIX) expression. We then describe the tumor distribution of this radiotracer ex vivo, in association with blood perfusion and known biomarkers of acidity, such as hypoxia, lactate dehydrogenase A, and CAIX. We find that the probe reveals metabolic variations between and within tumors, and discriminates between necrotic and living tumor areas