Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species.

BACKGROUND AND AIMS: Sugar concentration is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this study was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modelling approach. METHODS: We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of compounds other than sugar and starch, synthesis and hydrolysis of starch, and water dilution) involved in the accumulation of soluble sugars during fruit development. KEY RESULTS: Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwifruit). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared with all other species. CONCLUSIONS: Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the co-ordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not greatly affected by ethylene-associated events.

A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of a markedly low fructose-to-glucose ratio phenotype.

The concentrations of sugars in fruit vary with fruit development, environment and genotype. In general, there were weak correlations between the variations in sugar concentrations and the activities of enzymes directly related with the synthesis or degradation of sugars. This finding suggests that the relationships between enzyme activities and metabolites are often non-linear and are difficult to assess. To simulate the concentrations of sucrose, glucose, fructose and sorbitol during the development of peach fruit, a kinetic model of sugar metabolism was developed by taking advantage of recent profiling data. Cell compartmentation (cytosol and vacuole) was described explicitly, and data-driven enzyme activities were used to parameterize equations. The model correctly accounts for both annual and genotypic variations, which were observed in 10 genotypes derived from an interspecific cross. They provided important information on the mechanisms underlying the specification of phenotypic differences. In particular, the model supports the hypothesis that a difference in fructokinase affinity could be responsible for a low fructose-to-glucose ratio phenotype, which was observed in the studied population.

Organ-wide and ploidy-dependent regulation both contribute to cell-size determination: evidence from a computational model of tomato fruit.

The development of a new organ is the result of coordinated events of cell division and expansion, in strong interaction with each other. This study presents a dynamic model of tomato fruit development that includes cell division, endoreduplication, and expansion processes. The model is used to investigate the potential interactions among these developmental processes within the context of the neo-cellular theory. In particular, different control schemes (either cell-autonomous or organ-controlled) are tested and compared to experimental data from two contrasting genotypes. The model shows that a pure cell-autonomous control fails to reproduce the observed cell-size distribution, and that an organ-wide control is required in order to get realistic cell-size variations. The model also supports the role of endoreduplication as an important determinant of the final cell size and suggests that a direct effect of endoreduplication on cell expansion is needed in order to obtain a significant correlation between size and ploidy, as observed in real data.

Are compound leaves more complex than simple ones? A multi-scale analysis.

Background and Aims: The question of which cellular mechanisms determine the variation in leaf size has been addressed mainly in plants with simple leaves. It is addressed here in tomato taking into consideration the expected complexity added by the several lateral appendages making up the compound leaf, the leaflets. Methods: Leaf and leaflet areas, epidermal cell number and areas, and endoreduplication (co-) variations were analysed in Solanum lycopersicum considering heteroblastic series in a wild type (Wva106) and an antisense mutant, the Pro35S:Slccs52AAS line, and upon drought treatments. All plants were grown in an automated phenotyping platform, PHENOPSIS, adapted to host plants grown in 7 L pots. Key Results: Leaf area, leaflet area and cell number increased with leaf rank until reaching a plateau. In contrast, cell area slightly decreased and endoreduplication did not follow any trend. In the transgenic line, leaf area, leaflet areas and cell number of basal leaves were lower than in the wild type, but higher in upper leaves. Reciprocally, cell area was higher in basal leaves and lower in upper leaves. When scaled up at the whole sympodial unit, all these traits did not differ significantly between the transgenic line and the wild type. In response to drought, leaf area was reduced, with a clear dose effect that was also reported for all size-related traits, including endoreduplication. Conclusions: These results provide evidence that all leaflets have the same cellular phenotypes as the leaf they belong to. Consistent with results reported for simple leaves, they show that cell number rather than cell size determines the final leaf areas and that endoreduplication can be uncoupled from leaf and cell sizes. Finally, they re-question a whole-plant control of cell division and expansion in leaves when the Wva106 and the Pro35S:Slccs52AAS lines are compared.

Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development.

Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.

Impact of age on cytotoxic-induced ovarian failure in breast cancer treated with adjuvant chemotherapy and triptorelin.

AIM: This study analyzes our single-center, retrospective experience on 63 premenopausal breast cancer patients treated with monthly triptorelin and concomitant chemotherapy. PATIENTS & METHODS: Concomitant chemotherapy and triptorelin were adopted as part of premature ovarian failure prevention strategy. RESULTS: Age at diagnosis was the main factor influencing fertility preservation (p = 0.002). Compared with patients aged 41-45 years, the probability of menses resumption was almost threefold than for women aged 35-40 years, and significantly higher for women aged <35 years (hazard ratio: 9.0; p = 0.0001). The cumulative proportion among patients who resumed menses was 33.3% at 6 months, 75% at 12 months and 87.5% at 24 months. Seven patients attempted pregnancy, and five (71%) obtained healthy deliveries. CONCLUSION: We observed an acceptable rate of fertility preservation. Age at diagnosis influences fertility preservation.

Safety of eribulin mesylate and concomitant radiotherapy for metastatic breast cancer: a single-center experience.

AIM: This study evaluates, for the first time, the safety of eribulin in metastatic breast cancer patients concomitantly treated with palliative radiotherapy (RT). Patients & materials: A total of 17 patients were pretreated for metastatic breast cancer. Patients received eribulin mesylate and bone RT. RESULTS: The most frequent grade 3 hematologic adverse events were neutropenia (56%) and anemia (20%). Mean pain score decreased from 2 (baseline) to 0.7 (end of observation). Analgesic score remained stable (1.8 vs 1.6). Bone pain scores dropped within a few weeks and remained below baseline values throughout the analysis. The overall response rate was 29%, and the clinical benefit rate was 59%. CONCLUSION: Eribulin is characterized by a manageable safety profile also when combined with palliative RT.

Prognostic factors in patients receiving third line targeted therapy for metastatic renal cell carcinoma.

PURPOSE: Several prognostic models have been proposed for metastatic renal cell carcinoma but none has been validated in patients who receive third line targeted agents. We evaluated prognostic factors in patients with metastatic renal cell carcinoma who received a third line targeted agent. MATERIALS AND METHODS: We retrospectively reviewed data on 2,065 patients with clear cell metastatic renal cell carcinoma who were treated with targeted therapy at a total of 23 centers in Italy. Included in final analysis were 281 patients treated with 3 targeted agents. Overall survival was the main outcome. Cox proportional hazards regression followed by bootstrap validation was used to identify independent prognostic factors. RESULTS: Three clinical characteristics (ECOG performance status greater than 1, metastasis at diagnosis and liver metastasis) and 2 biochemical factors (hemoglobin less than the lower limit of normal and neutrophil count greater than the upper limit of normal, respectively) were prognostic. Patients were classified into 3 risk categories, including low-zero or 1, intermediate-2 and high risk-more than 2 risk factors. Median overall survival was 19.7, 10.1 and 5.5 months, and 1-year overall survival was 71%, 43% and 15%, respectively. The major limitation was the retrospective nature of this study and absent external validation. CONCLUSIONS: This nomogram included clinical and biochemical prognostic factors. In clinical trials it may be useful to select patients and define the prognosis.

Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios.

BACKGROUND: Fruit taste is largely affected by the concentration of soluble sugars and organic acids and non-negligibly by fructose concentration, which is the sweetest-tasting sugar. To date, many studies investigating the sugars in fruit have focused on a specific sugar or enzyme and often on a single variety, but only a few detailed studies addressing sugar metabolism both as a whole and dynamic system are available. In commercial peach fruit, sucrose is the main sugar, followed by fructose and glucose, which have similar levels. Interestingly, low fructose-to-glucose ratios have been observed in wild peach accessions. A cross between wild peach and commercial varieties offers an outstanding possibility to study fruit sugar metabolism. RESULTS: This work provides a large dataset of sugar composition and the capacities of enzymes that are involved in sugar metabolism during peach fruit development and its genetic diversity. A large fraction of the metabolites and enzymes involved in peach sugar metabolism were assayed within a peach progeny of 106 genotypes, of which one quarter displayed a low fructose-to-glucose ratio. This profiling was performed at six stages of growth using high throughput methods. Our results permit drawing a quasi-exhaustive scheme of sugar metabolism in peach. The use of a large number of genotypes revealed a remarkable robustness of enzymatic capacities across genotypes and years, despite strong variations in sugar composition, in particular the fructose-to-glucose ratio, within the progeny. A poor correlation was also found between the enzymatic capacities and the accumulation rates of metabolites. CONCLUSIONS: These results invalidate the hypothesis of the straightforward enzymatic control of sugar concentration in peach fruit. Alternative hypotheses concerning the regulation of fructose concentration are discussed based on experimental data. This work lays the foundation for a comprehensive study of the mechanisms involved in sugar metabolism in developing fruit.

Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.

Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. An interesting prediction of our model, supported by the experimental data, is that high growth rates are not necessarily accompanied by low growth yields. The resource allocation strategies enabling high-rate, high-yield growth of E. coli lead to a higher saturation of enzymes and ribosomes, and thus to a more efficient utilization of proteomic resources. Our model thus contributes to a fundamental understanding of the quantitative relationship between rate and yield in E. coli and other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.

U-CHANGE Project: a multidimensional consensus on how clinicians, patients and caregivers may approach together the new urothelial cancer scenario.

Introduction: Advanced urothelial carcinoma remains aggressive and very hard to cure, while new treatments will pose a challenge for clinicians and healthcare funding policymakers alike. The U-CHANGE Project aimed to redesign the current model of care for advanced urothelial carcinoma patients to identify limitations ("as is" scenario) and recommend future actions ("to be" scenario). Methods: Twenty-three subject-matter experts, divided into three groups, analyzed the two scenarios as part of a multidimensional consensus process, developing statements for specific domains of the disease, and a simplified Delphi methodology was used to establish consensus among the experts. Results: Recommended actions included increasing awareness of the disease, increased training of healthcare professionals, improvement of screening strategies and care pathways, increased support for patients and caregivers and relevant recommendations from molecular tumor boards when comprehensive genomic profiling has to be provided for appropriate patient selection to ad hoc targeted therapies. Discussion: While the innovative new targeted agents have the potential to significantly alter the clinical approach to this highly aggressive disease, the U-CHANGE Project experience shows that the use of these new agents will require a radical shift in the entire model of care, implementing sustainable changes which anticipate the benefits of future treatments, capable of targeting the right patient with the right agent at different stages of the disease.

Sunitinib-induced hyperparathyroidism: a possible mechanism to altered bone homeostasis.

BACKGROUND: Sunitinib malate is an orally bioavailable tyrosine kinase inhibitor that is active against many tyrosine kinase receptors involving crucial pathways in both healthy tissues and malignant tissues. Because its use in clinical practice is quite recent, many of its possible side effects remain unknown. In this report, the authors describe the incidence of new-onset hyperparathyroidism in a cohort of patients with metastatic renal cell carcinoma who received treatment with sunitinib. METHODS: Twenty-six patients who received first-line sunitinib for metastatic renal cell carcinoma were enrolled in this study for a mineral and parathyroid function assessment. Plasma levels of intact parathyroid hormone; serum levels of calcium, phosphorus, 25-hydroxyvitamin D(3), and 1,25-dihydrovitamin D(3); and urinary 24-hour calcium and phosphorus excretion all were measured in each patient. Biochemical evaluations were performed before the beginning of treatment and at the end of each sunitinib treatment period. RESULTS: Eighteen of 26 patients (69.2%) developed hyperparathyroidism with normal serum calcium levels, and 6 of them developed hypophosphatemia. Patients presented with a mean elevation of parathyroid hormone after 2.2 cycles of sunitinib. The levels of 25-OH vitamin D(3) were stable over the course of treatment, whereas 1,25-OH vitamin D(3) levels were increased in 5 hyperparathyroid patients. Those who presenting with elevated parathyroid hormone levels had low or undetectable urinary calcium levels. Parathyroid hormone elevation usually persisted but did not progress during long-term therapy with sunitinib. Permanent treatment interruption resulted in a resolution of hyperparathyroidism. CONCLUSIONS: Hyperparathyroidism developed in an high percentage of patients on sunitinib. Therefore, the authors concluded that sunitinib may affect parathyroid function and bone mineral homeostasis, possibly resulting in abnormal bone remodeling.

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.

Gene regulatory networks consist of direct interactions, but also include indirect interactions mediated by metabolism. We investigate to which extent these indirect interactions arising from metabolic coupling influence the dynamics of the system. To this end, we build a qualitative model of the gene regulatory network controlling carbon assimilation in Escherichia coli, and use this model to study the changes in gene expression following a diauxic shift from glucose to acetate. In particular, we compare the relative variation in the steady-state concentrations of enzymes and transcription regulators during growth on glucose and acetate, as well as the dynamic response of gene expression to the exhaustion of glucose and the subsequent assimilation of acetate. We find significant differences between the dynamics of the system in the absence and presence of metabolic coupling. This shows that interactions arising from metabolic coupling cannot be ignored when studying the dynamics of gene regulatory networks.

The national COVID-19 vaccination campaign targeting the extremely vulnerable: the Florence Medical Oncology Unit experience in patients with cancer.

BACKGROUND: International and national oncology societies had released recommendations in favor of COVID-19 vaccination in cancer patients. In the context of the national vaccination campaign targeting the so called extremely vulnerable, we aimed to assess the safety and efficacy of the mRNA vaccines in a cohort of 623 patients. METHODS: Between March 26 and April 04, 2021, the Pfizer and BioNTech BNT162b2 mRNA and the Moderna mRNA-1273 vaccines were given as a two-dose prime-boost regimen. Starting on September 25th 2021 a third dose was offered to patients in whom a suboptimal immunogenicity with COVID-19 vaccination could be expected. Safety assessments were performed by phone call 7 days after each dose. Electronic health records were accessed to review demographic information, disease history, treatment detail, and outcome events of participants patients'. FINDINGS: No toxicities were reported in 63.7%, 54%, and in 48.7% patients with cancer after each dose. Mild-to-moderate pain at the injection site was the most commonly adverse event. After the second dose, 46% of the 610 patients reported toxicity, with more systemic side-effects observed. Fever was reported in 45% of patients, with a temperature ≥ 38 °C in 21.4% of them. Of the 335 patients receiving a third vaccine dose, 51% reported toxicity, with 13% of patients reporting more than one effect. Logistic regression analysis reported mixed results, with limited variables or categories reporting a significant odd ratio. The type of vaccine reported a significant value at first dose (OR = 0.12; CI 0.52, 0.26; p = 0.00). Thirty-four cases of COVID-19 infection were reported with only one patient requiring a short-term hospitalization for monitoring. INTERPRETATION: The safety profile of the mRNA vaccines does not raise any specific concerns and support prioritization of vaccination for cancer patients.

The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.

Gene regulatory networks consist of direct interactions but also include indirect interactions mediated by metabolites and signaling molecules. We describe how these indirect interactions can be derived from a model of the underlying biochemical reaction network, using weak time-scale assumptions in combination with sensitivity criteria from metabolic control analysis. We apply this approach to a model of the carbon assimilation network in Escherichia coli. Our results show that the derived gene regulatory network is densely connected, contrary to what is usually assumed. Moreover, the network is largely sign-determined, meaning that the signs of the indirect interactions are fixed by the flux directions of biochemical reactions, independently of specific parameter values and rate laws. An inversion of the fluxes following a change in growth conditions may affect the signs of the indirect interactions though. This leads to a feedback structure that is at the same time robust to changes in the kinetic properties of enzymes and that has the flexibility to accommodate radical changes in the environment.

Reducing a model of sugar metabolism in peach to catch different patterns among genotypes.

Several studies have been conducted to understand the dynamic of primary metabolisms in fruit by translating them into mathematics models. An ODE kinetic model of sugar metabolism has been developed by Desnoues et al. (2018) to simulate the accumulation of different sugars during peach fruit development. Two major drawbacks of this model are (a) the number of parameters to calibrate and (b) its integration time that can be long due to non-linearity and time-dependent input functions. Together, these issues hamper the use of the model for a large panel of genotypes, for which few data are available. In this paper, we present a model reduction scheme that explicitly addresses the specificity of genetic studies in that: (i) it yields a reduced model that is adapted to the whole expected genetic diversity (ii) it maintains network structure and variable identity, in order to facilitate biological interpretation. The proposed approach is based on the combination and the systematic evaluation of different reduction methods. Thus, we combined multivariate sensitivity analysis, structural simplification and timescale-based approaches to simplify the number and the structure of ordinary differential equations of the model. The original and reduced models were compared based on three criteria, namely the corrected Aikake Information Criterion (AICC), the calibration time and the expected error of the reduced model over a progeny of virtual genotypes. The resulting reduced model not only reproduces the predictions of the original one but presents many advantages including a reduced number of parameters to be estimated and shorter calibration time, opening new promising perspectives for genetic studies and virtual breeding. The validity of the reduced model was further evaluated by calibration on 30 additional genotypes of an inter-specific peach progeny for which few data were available.

Modeling lymphocyte homing and encounters in lymph nodes.

BACKGROUND: The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research. RESULTS: In this paper, we present a hybrid discrete/continuous model of the lymph node, accounting for differences in cell velocity and chemotactic response, influenced by the spatial compartmentalization of the lymph node and the regulation of cells migration, encounter, and antigen presentation during the inflammation process. CONCLUSION: Our model reproduces the correct timing of an immune response, including the observed time delay between duplication of T helper cells and duplication of B cells in response to antigen exposure. Furthermore, we investigate the consequences of the absence of dendritic cells at different times during infection, and the dependence of system dynamics on the regulation of lymphocyte exit from lymph nodes. In both cases, the model predicts the emergence of an impaired immune response, i.e., the response is significantly reduced in magnitude. Dendritic cell removal is also shown to delay the response time with respect to normal conditions.

Leaf Production and Expansion: A Generalized Response to Drought Stresses from Cells to Whole Leaf Biomass-A Case Study in the Tomato Compound Leaf.

It is clearly established that there is not a unique response to soil water deficit but that there are as many responses as soil water deficit characteristics: Drought intensity, drought duration, and drought position during plant cycle. For a same soil water deficit, responses can also differ on plant genotype within a same species. In spite of this variability, at least for leaf production and expansion processes, robust tendencies can be extracted from the literature when similar watering regimes are compared. Here, we present response curves and multi-scale dynamics analyses established on tomato plants exposed to different soil water deficit treatments. Results reinforce the trends already observed for other species: Reduction in plant leaf biomass under water stress was due to reduction in individual leaf biomass and areas whereas leaf production and specific leaf area were not affected. The dynamics of leaf expansion was modified both at the leaf and cell scales. Cell division and expansion were reduced by drought treatments as well as the endoreduplication process. Combining response curves analyses together with dynamic analyses of tomato compound leaf growth at different scales not only corroborate results on simple leaf responses to drought but also increases our knowledge on the cellular mechanisms behind leaf growth plasticity.

Integrating Physiology and Architecture in Models of Fruit Expansion.

Architectural properties of a fruit, such as its shape, vascular patterns, and skin morphology, play a significant role in determining the distributions of water, carbohydrates, and nutrients inside the fruit. Understanding the impact of these properties on fruit quality is difficult because they develop over time and are highly dependent on both genetic and environmental controls. We present a 3D functional-structural fruit model that can be used to investigate effects of the principle architectural properties on fruit quality. We use a three step modeling pipeline in the OpenAlea platform: (1) creating a 3D volumetric mesh representation of the internal and external fruit structure, (2) generating a complex network of vasculature that is embedded within this mesh, and (3) integrating aspects of the fruit's function, such as water and dry matter transport, with the fruit's structure. We restrict our approach to the phase where fruit growth is mostly due to cell expansion and the fruit has already differentiated into different tissue types. We show how fruit shape affects vascular patterns and, as a consequence, the distribution of sugar/water in tomato fruit. Furthermore, we show that strong interaction between tomato fruit shape and vessel density induces, independently of size, an important and contrasted gradient of water supply from the pedicel to the blossom end of the fruit. We also demonstrate how skin morphology related to microcracking distribution affects the distribution of water and sugars inside nectarine fruit. Our results show that such a generic model permits detailed studies of various, unexplored architectural features affecting fruit quality development.

Complete response in metastatic renal cell carcinoma after radiotherapy and everolimus: a clinical case and review of the literature.

We report the case of a man affected by renal cell carcinoma with vertebral metastases, who presented a radiological complete response after systemic treatment with everolimus.