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The evolution of diabetes in the male leptin receptor-deficient (fa/fa) Zucker diabetic fatty (ZDF) rat is associated with disruption of normal islet architecture, beta-cell degranulation, and increased beta-cell death. It is unknown whether these changes precede or develop as a result of the increasing plasma glucose, or whether the increased beta-cell death can be prevented. Early intervention with thiazolidinediones prevents disruption of the islet architecture. To determine the specific effects of rosiglitazone (RSG) on beta-cell mass dynamics, male fa/fa (obese) and +/fa or +/+ (lean) rats age 6 weeks were fed either chow (control group [CN]) or chow mixed with rosiglitazone (RSG group) at a dosage of 10 micromol. kg(-1) body wt.day(-1). Rats were killed after 0, 2, 4, 6, or 10 weeks of treatment (at age 6, 8, 10, 12, or 16 weeks). Plasma glucose increased from 8.9 +/- 0.4 mmol/l at 0 weeks to 34.2 +/- 1.8 mmol/l (P = 0.0001) at 6 weeks of treatment in obese CN rats and fell from 8.0 +/- 0.3 to 6.3 +/- 0.4 mmol/l in obese RSG rats (P = 0.02). beta-cell mass fell by 51% from 2 to 6 weeks of treatment (ages 8-12 weeks) in obese CN rats (6.9 +/- 0.9 to 3.4 +/- 0.5 mg; P < 0.05), whereas beta-cell mass was unchanged in obese RSG rats. At 10 weeks of treatment (age 16 weeks), beta-cell mass in obese CN rats was only 56% of that of obese RSG rats (4.4 +/- 0.4 vs. 7.8 +/- 0.3 mg, respectively; P = 0.0001). The beta-cell replication rate fell from a baseline value of 0.95 +/- 0.12% in lean rats and 0.94 +/- 0.07% in obese rats (at 0 weeks) to approximately 0.3-0.5% in all groups by 6 weeks of treatment (age 12 weeks). After 10 weeks of treatment, beta-cell replication was higher in obese RSG rats than in CN rats (0.59 +/- 0.14 vs. 0.28 +/- 0.05%, respectively; P < 0.02). Application of our mass balance model of beta-cell turnover indicated that net beta-cell death was fivefold higher in obese CN rats as compared with RSG rats after 6 weeks of treatment (age 12 weeks). The increase in beta-cell death in obese CN rats during the 6-week observation period was well correlated with the increase in plasma glucose (r2 = 0.90, P < 0.0001). These results suggest that the development of hyperglycemia in ZDF rats is concomitant with increasing net beta-cell death. beta-cell proliferation compensates for the increased beta-cell loss at a time when plasma glucose is moderately elevated, but compensation ultimately fails and the plasma glucose levels increase beyond approximately 20 mmol/l. Treatment with rosiglitazone, previously shown to reduce insulin resistance, prevents the loss of beta-cell mass in obese ZDF rats by maintaining beta-cell proliferation and preventing increased net beta-cell death. [ABSTRACT FROM AUTHOR]

The genus Macadamia in the Proteaceae family includes four species native to Australia. Two of the four species, M. integrifolia and M. tetraphylla , have recently been utilized to generate domesticated macadamia varieties, grown for their edible nuts. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of the nuclear genome (based upon concatenated nuclear gene CDS and SNPs). The two larger species ( M. integrifolia and M. tetraphylla ) formed a clade, that had diverged from a clade including the smaller species ( M. ternifolia and M. jansenii ). The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributed M. integrifolia while the rare M. jansenii showed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades, including genotypes from different species. This suggests extensive reticulate evolution in Macadamia despite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species that have large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting the longer distance pollen movement. This improved understanding of the distribution of diversity in Macadamia will aid in the conservation of these rare species now found in highly fragmented rainforest remnants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Manatunga, Furtado, Topp, Alam, Mason, Kharabian-Masouleh and Henry.)

Domestic storage conditions can have a significant impact on the composition of phytochemicals and sugars in stone fruits. This study aimed to evaluate the effect of two domestic storage temperatures (4 and 23 °C) on the physicochemical properties, phytochemical composition, and sugars of 'Rubycot' (RC) plumcot, a novel stone fruit variety, and 'Queen Garnet' (QG) plum. Initially, RC had a lower total anthocyanin concentration (TAC) than QG, but TAC in RC increased significantly ( p < 0.05) during storage, peaking at +95% after 7 days at 23 °C, while QG reached +60% after 14 days. At 4 °C, TAC increased for both varieties (RC +30%, QG +27%). RC had a higher initial total phenolic content (TPC), which also increased for both fruits. QG had a significantly higher initial total quercetin concentration (TQC), increasing by 40% ( p < 0.05) at 23 °C. The initial total carotenoid concentration in QG was higher than that in RC, but after 10 days at 23 °C, RC had a higher carotenoid concentration than QG. Both varieties showed similar sugar profiles, with QG starting higher but decreasing over time at both storage temperatures. Results from this study showed that ambient storage significantly increases total anthocyanins, total quercetins, and TPC in RC and QG. However, it is important to evaluate the textural and sensory properties of stored RC and QG in terms of consumer acceptability of the stored fruits.

Phase Ib trials are common in oncology development but often are not powered for statistical significance. Go/no-go decisions are largely driven by observed trends in response data. We applied a bootstrapping method to systematically compare tumor dynamic end points to historical control data to identify drugs with clinically meaningful efficacy. A proprietary mathematical model calibrated to phase Ib anti-PD-1 therapy trial data (KEYNOTE-001) was used to simulate thousands of phase Ib trials (n = 30) with a combination of anti-PD-1 therapy and four novel agents with varying efficacy. A redacted bootstrapping method compared these results to a simulated phase III control arm (N = 511) while adjusting for differences in trial duration and cohort size to determine the probability that the novel agent provides clinically meaningful efficacy. Receiver operating characteristic (ROC) analysis showed strong ability to separate drugs with modest (area under ROC [AUROC] = 83%), moderate (AUROC = 96%), and considerable efficacy (AUROC = 99%) from placebo in early-phase trials (n = 30). The method was shown to effectively move drugs with a range of efficacy through an in silico pipeline with an overall success rate of 93% and false-positive rate of 7.5% from phase I to phase III. This model allows for effective comparisons of tumor dynamics from early clinical trials with more mature historical control data and provides a framework to predict drug efficacy in early-phase trials. We suggest this method should be employed to improve decision making in early oncology trials., (© 2024 Merck Sharp & Dohme LLC and The Author(s). CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.)

Therapies targeting the programmed cell death protein-1/programmed death-ligand 1 (PD-L1) (abbreviated as PD-(L)1) axis are a significant advancement in the treatment of many tumor types. However, many patients receiving these agents fail to respond or have an initial response followed by cancer progression. For these patients, while subsequent immunotherapies that either target a different axis of immune biology or non-immune combination therapies are reasonable treatment options, the lack of predictive biomarkers to follow-on agents is impeding progress in the field. This review summarizes the current knowledge of mechanisms driving resistance to PD-(L)1 therapies, the state of biomarker development along this axis, and inherent challenges in future biomarker development for these immunotherapies. Innovation in the development and application of novel biomarkers and patient selection strategies for PD-(L)1 agents is required to accelerate the delivery of effective treatments to the patients most likely to respond., Competing Interests: Competing interests: SW—Salary and employment: Kite Pharma, Gilead; Consulting fees: SciSpot; Stock ownership: Kite Pharma, Gilead. JCB—Salary and employment: Precede Biosciences; Ownership: JCarl Consulting, LLC; Stock Ownership: AstraZeneca. CG-B—Salary and employment: Bristol Myers Squibb. Stock ownership: Bristol Myers Squibb. KAS—Consulting fees: Shattuck Labs, EMD Serono, Clinica Alemana de Santiago, Genmab, Takeda, Merck Sharpe & Dohme, Bristol Myers Squibb, AstraZeneca, Agenus, Repertoire; Fees for non-CE services: Bristol Myers Squibb, Fluidigm Corporation, Genmab, Merck, Takeda; Contracted research: Navigate Biopharma, Tesaro/GSK, Moderna Inc., Pierre-Fabre, Takeda, Surface Oncology, Merck Sharpe & Dohme, Bristol Myers Squibb, AstraZeneca, Ribon Therapeutics, Akoya Biosciences, Boehringer-Ingelheim, Eli Lilly. JMT—Research funding: Bristol Myers Squibb, Akoya Biosciences; Consulting fees: Bristol Myers Squibb, Roche/Genentech, Merck & Co., AstraZeneca, Regeneron; Stock ownership: Akoya Biosciences. BT—Salary and employment: Merck & Co.; Stock ownership: Merck & Co. AS—Salary and employment: Generate Biomedicines; Stock ownership, Generate Biomedicines, Merck & Co., Allogene. AM—Nothing to disclose. SITC Staff: FD, PJI—Nothing to disclose., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The Response Evaluation Criteria in Solid Tumors (RECIST)-based outcomes, such as objective response rate (ORR) or progression free survival (PFS), are standard outcomes for early oncology trials. These indices provide a black-and-white interpretation of response to therapy. We propose that lesion-level analysis and mechanism-based pharmacodynamic endpoints may provide a more informative index of response to therapy. Accounting for "shades of gray" in lesion-level response assessments may reduce bias in go/no-go decisions and biomarker analyses for novel oncology compounds and discontinuation decisions for individual patients., Competing Interests: Declaration of interests B.T. is an employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, US. A.S. is an employee of Generate Biomedicine and owns stock in Merck. J.W. is a consultant for Apricity; Ascentage Pharma; AstraZeneca; BeiGene; Bicara Therapeutics; Bristol Myers Squibb; Chugai, Daiichi Sankyo; Dragonfly; Imvaq; Larkspur; Psioxus, Tizona; and Trishula Therapeutics. J.W. received grant/research support from Bristol Myers Squibb and Sephora. J.W. has equity in Apricity, Arsenal IO; Ascentage; CellCarta; Imvaq; Linneaus, Larkspur; Georgiamune; Maverick; Tizona Therapeutics; and Xenimmune., (Copyright © 2023 Elsevier Inc. All rights reserved.)

RECISTv1.1 (Response Evaluation Criteria In Solid Tumors) is the most commonly used response grading criteria in early oncology trials. In this perspective, we argue that RECISTv1.1 is ambiguous regarding lesion-to-lesion variation that can introduce bias in decision making. We show theoretical examples of how lesion-to-lesion variability causes bias in RECISTv1.1, leading to misclassification of patient response. Next, we review immune checkpoint inhibitor (ICI) clinical trial data and find that lesion-to-lesion heterogeneity is widespread in ICI-treated patients. We illustrate the implications of ignoring lesion-to-lesion heterogeneity in interpreting biomarker data, selecting treatments for patients with progressive disease, and go/no-go decisions in drug development. Further, we propose that Quantitative Systems Pharmacology (QSP) models can aid in developing better metrics of patient response and treatment efficacy by capturing patient responses robustly by considering lesion-to-lesion heterogeneity. Overall, we believe patient response evaluation with an appreciation of lesion-to-lesion heterogeneity can potentially improve decision-making at the early stage of oncology drug development and benefit patient care., Competing Interests: Author BT reports employment at the company Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States, and is a shareholder in Merck & Co., Inc., Kenilworth, NJ, United States. Author RK was employed by the company Vantage Research Inc. Vantage Research was engaged by MSD as a Contract Research Organization. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Kumar, Qi, Cao and Topp.)

Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. Chromosome level genome assemblies using sequence contigs generated from long read sequencing have involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (HiFi; PacBio) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii, a genome that has been used as a model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig (six with telomere repeats at both ends) and the other six assembled from two to four main contigs. The small number of chromosome breaks appears to be the result of highly repetitive regions including ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now appears possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed., (© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zakeel, Alam, Geering, Topp and Akinsanmi.)

Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii , being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here, we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive. Completeness assessment revealed that the assembly covered -97.1% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism, and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies., Competing Interests: The Authors did not report any conflict of interest., (© 2021 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd.)

Background: Disease progression is often considered a binary state reflecting presence or absence of response. Meaningful heterogeneity between metastatic sites of a given patient may exist, however, and may impact therapeutic outcomes. To characterize the heterogeneity of progression with immunotherapy, we evaluated lesion-level dynamics of pembrolizumab-treated patients across three tumor types., Patients and Methods: Individual metastatic lesion dynamics were analyzed retrospectively in patients with advanced melanoma, non-small-cell lung cancer (NSCLC), and gastric or gastroesophageal junction (G/GEJ) cancer who received pembrolizumab in KEYNOTE-001 or KEYNOTE-059. Primary progression was defined as radiologic progression as per RECIST v1.1 occurring at the first on-treatment study scan (∼9-12 weeks, +2-week window) and secondary progression as progression occurring beyond the first scan (∼14 weeks and beyond). The change in sum of target lesions and of individual lesions was examined, as were patterns and timing of progression., Results: 9239 individual lesions from 1194 patients were analyzed. Among patients with primary progression [39% (200/511) of patients with melanoma, 41% (179/432) with NSCLC, 61% (154/251) with G/GEJ cancer], most patients (51%-63%) had a mixture of growing, stable, and shrinking lesions. Despite overall primary progression, a minority of patients (19%-25%) had tumor growth at every metastatic site and 17%-32% had ≥1 shrinking lesion. Among patients with secondary progression [22% (113/511) of patients with melanoma, 27% (117/432) with NSCLC, 18% (44/251) with G/GEJ cancer], few patients had rebound growth (>20% increase in diameter from nadir) in all lesions whereas the majority (74%-84%) had sustained regression in ≥1 lesion., Conclusions: Lesion-level heterogeneity at the time of disease progression was common in pembrolizumab-treated patients, with many patients demonstrating ongoing disease control in a subset of tumor sites. These results may inform clinical decision-making, trial design, and tumor sampling in the future., Competing Interests: Disclosure BGT reports employment at Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA, and is a shareholder in Merck & Co., Inc., Kenilworth, NJ, USA. KT has declared no conflicts of interest. DPDA reports employment at Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA, and is a shareholder in Merck & Co., Inc., Kenilworth, NJ, USA. AS reports employment at Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA, and is a shareholder in Merck & Co., Inc., Kenilworth, NJ, USA. MDH reports grants from Bristol Myers Squibb; nonfinancial support from AstraZeneca and Bristol Myers Squibb; and personal fees from Achilles; Arcus AstraZeneca; Blueprint Medicines; Bristol Myers Squibb; Genentech/Roche; Immunai; Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA; Mirati; Nektar; Pact Pharma; Shattuck Labs; Syndax; Janssen; and Regeneron; as well as equity options from Immunai, Shattuck Labs, and Arcus. A patent filed by Memorial Sloan Kettering related to the use of tumor mutational burden to predict response to immunotherapy (PCT/US2015/062208) is pending and licensed by PGDx., (Copyright © 2021 Merck Sharp & Dohme Corp., The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Immune checkpoint inhibitors, administered as single agents, have demonstrated clinical efficacy. However, when treating cold tumors, different combination strategies are needed. This work aims to develop a semi-mechanistic model describing the antitumor efficacy of immunotherapy combinations in cold tumors. Tumor size of mice treated with TC-1/A9 non-inflamed tumors and the drug effects of an antigen, a toll-like receptor-3 agonist (PIC), and an immune checkpoint inhibitor (anti-programmed cell death 1 antibody) were modeled using Monolix and following a middle-out strategy. Tumor growth was best characterized by an exponential model with an estimated initial tumor size of 19.5 mm 3 and a doubling time of 3.6 days. In the treatment groups, contrary to the lack of response observed in monotherapy, combinations including the antigen were able to induce an antitumor response. The final model successfully captured the 23% increase in the probability of cure from bi-therapy to triple-therapy. Moreover, our work supports that CD8 + T lymphocytes and resistance mechanisms are strongly related to the clinical outcome. The activation of antigen-presenting cells might be needed to achieve an antitumor response in reduced immunogenic tumors when combined with other immunotherapies. These models can be used as a platform to evaluate different immuno-oncology combinations in preclinical and clinical scenarios.

A quantitative systems pharmacology model for metastatic melanoma was developed for immuno-oncology with the goal of predicting efficacy of combination checkpoint therapy with pembrolizumab and ipilimumab. This literature-based model is developed at multiple scales: (i) tumor and immune cell interactions at a lesion level; (ii) multiple heterogeneous target lesions, nontarget lesion growth, and appearance of new metastatic lesion at a patient level; and (iii) interpatient differences at a population level. The model was calibrated to pembrolizumab and ipilimumab monotherapy in patients with melanoma from Robert et al., specifically, waterfall plot showing target lesion response and overall response rate (Response Evaluation Criteria in Solid Tumors [RECIST] version 1.1), which additionally considers nontarget lesion growth and appearance of new metastatic lesions. We then used the model to predict waterfall and RECIST version 1.1 for combination treatment reported in Long et al. A key insight from this work was that nontarget lesions growth and appearance of new metastatic lesion contributed significantly to disease progression, despite reduction in target lesions. Further, the lesion level simulations of combination therapy show substantial efficacy in warm lesions (intermediary immunogenicity) but limited advantage of combination in both cold and hot lesions (low and high immunogenicity). Because many patients with metastatic disease are expected to have a mixture of these lesions, disease progression in such patients may be driven by a subset of cold lesions that are unresponsive to checkpoint inhibitors. These patients may benefit more from the combinations which include therapies to target cold lesions than double checkpoint inhibitors., (© 2021 Merck Sharp & Dohme Corporation & Vantage Research LLC. CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.)

Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii , was also compared with three other Macadamia species, as well as avocado ( Persea americana ) and jojoba ( Simmondsia chinensis ). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

Background: Anti-programmed cell death 1 (PD-1)/programmed death-ligand 1 (PD-L1) monoclonal antibodies (mAbs) show remarkable clinical anti-tumour efficacy. However, rational combinations are needed to extend the clinical benefit to primary resistant tumours. The design of such combinations requires the identification of the kinetics of critical immune cell populations in the tumour microenvironment., Methods: In this study, we compared the kinetics of immune cells in the tumour microenvironment upon treatment with immunotherapy combinations with different anti-tumour efficacies in the non-inflamed tumour model TC-1/A9. Tumour-bearing C57BL/6J mice were treated with all possible combinations of a human papillomavirus (HPV) E7 long peptide, polyinosinic-polycytidylic acid (PIC) and anti-PD-1 mAb. Tumour growth and kinetics of the relevant immune cell populations were assessed over time. The involvement of key immune cells was confirmed by depletion with mAbs and immunophenotyping with multiparametric flow cytometry., Results: The maximum anti-tumour efficacy was achieved after intratumoural administration of HPV E7 long peptide and PIC combined with the systemic administration of anti-PD-1 mAb. The intratumoural immune cell kinetics of this combination was characterised by a biphasic immune response. An initial upsurge of proinflammatory myeloid cells led to a further rise in effector CD8 + T lymphocytes at day 8. Depletion of either myeloid cells or CD8 + T lymphocytes diminished the anti-tumour efficacy of the combination., Conclusions: The anti-tumour efficacy of a successful immunotherapy combination in a non-inflamed tumour model relies on an early inflammatory process that remodels the myeloid cell compartment.

Due to high perishability, plums are harvested at an early stage of maturity to extend postharvest storage life. Storage time and temperature can significantly affect the phytochemical and sugar composition of plums, altering their palatability and nutritional quality. In this study, variations in physiochemical properties (total soluble solids (TSS), titratable acidity (TA), color (chroma and hue angle)), phytochemical composition (total phenolic content (TPC), total anthocyanin content (TAC), and carotenoids), and sugars in three different tissues of the Queen Garnet plum (QGP) during storage at two common domestic storage temperatures (4 and 23 °C) were evaluated. There was an increase ( p > 0.05) in TSS and a reduction ( p < 0.05) in TA of the outer flesh at 23 °C. Chroma values of all the tissues reduced ( p < 0.05) at 23 °C. At 4 °C, chroma values fluctuated between storage days. The TAC of the peel was the highest ( p < 0.05) among the different tissues and continued to increase up to 10 days of storage at 23 °C (3-fold increase). At 4 °C, the highest ( p < 0.05) TAC (peel) was observed after 14 days of storage (1.2-fold increase). TPC showed similar results. The highest ( p < 0.05) TPC was recorded in the peel after 10 days of storage at 23 °C (2.3-fold increase) and after 14 days of storage at 4 °C (1.3-fold increase), respectively. Total carotenoids in the flesh samples at both storage temperatures were reduced ( p < 0.05) after 14 days. Total sugars also decreased during storage. The results of the present study clearly showed that common domestic storage conditions can improve the nutritional quality of plums by increasing the content of bioactive anthocyanins and other phenolic compounds. However, the increase in phytochemicals needs to be counterbalanced with the decrease in total sugars and TA potentially affecting the sensory attributes of the plums.

Background: Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample., Results: Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements., Conclusions: The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies., (© The Author(s) 2020. Published by Oxford University Press GigaScience.)

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics., (Copyright © 2020 Nock et al.)

Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more diverse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) Macadamia integrifolia , (ii) M. tetraphylla , and (iii) M. jansenii and M. ternifolia , and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one M. integrifolia and four M. tetraphylla accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure examples of one of the four species and 15 as hybrids of M. integrifolia and M. tetraphylla . The admixed accessions showed the highest genetic diversity followed by M. integrifolia , while M. ternifolia and M. jansenii accessions were the least diverse. Mantel test analysis showed a significant correlation between genetic and geographic distance for M. integrifolia (r = 0.51, p = 0.05) and a positive but not significant correlation for M. tetraphylla (r = 0.45, p = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.

Background: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme., Results: Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs., Conclusions: These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.

Quantitative systems pharmacology (QSP) approaches have been increasingly applied in the pharmaceutical since the landmark white paper published in 2011 by a National Institutes of Health working group brought attention to the discipline. In this perspective, we discuss QSP in the context of other modeling approaches and highlight the impact of QSP across various stages of drug development and therapeutic areas. We discuss challenges to the field as well as future opportunities., (© 2019 Takeda California, Inc CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of the American Society for Clinical Pharmacology and Therapeutics.)