APSIM-based modeling approach to understand sorghum production environments in Mali.

Sorghum production system in the semi-arid region of Africa is characterized by low yields which are generally attributed to high rainfall variability, poor soil fertility, and biotic factors. Production constraints must be well understood and quantified to design effective sorghum-system improvements. This study uses the state-of-the-art in silico methods and focuses on characterizing the sorghum production regions in Mali for drought occurrence and its effects on sorghum productivity. For this purpose, we adapted the APSIM-sorghum module to reproduce two cultivated photoperiod-sensitive sorghum types across a latitude of major sorghum production regions in Western Africa. We used the simulation outputs to characterize drought stress scenarios. We identified three main drought scenarios: (i) no-stress; (ii) early pre-flowering drought stress; and (iii) drought stress onset around flowering. The frequency of drought stress scenarios experienced by the two sorghum types across rainfall zones and soil types differed. As expected, the early pre-flowering and flowering drought stress occurred more frequently in isohyets < 600 mm, for the photoperiod-sensitive, late-flowering sorghum type. In isohyets above 600 mm, the frequency of drought stress was very low for both cultivars. We quantified the consequences of these drought scenarios on grain and biomass productivity. The yields of the highly-photoperiod-sensitive sorghum type were quite stable across the higher rainfall zones > 600 mm, but was affected by the drought stress in the lower rainfall zones < 600 mm. Comparatively, the less photoperiod-sensitive cultivar had notable yield gain in the driest regions < 600 mm. The results suggest that, at least for the tested crop types, drought stress might not be the major constraint to sorghum production in isohyets > 600 mm. The findings from this study provide the entry point for further quantitative testing of the Genotype × Environment × Management options required to optimize sorghum production in Mali. Supplementary Information: The online version contains supplementary material available at 10.1007/s13593-023-00909-5.

Phenotypic plasticity of plant traits contributing to grain and biomass yield of dual-purpose sorghum.

MAIN CONCLUSION: Plant traits of interest for sorghum breeders to develop dual-purpose varieties are stem diameter, flag leaf size, crop cycle, and number of grains per panicle. To develop dual-purpose varieties, breeders need to improve traits linked both to grain and biomass production. To identify these traits, we studied the phenotypic plasticity of eighteen traits and the performance of ten contrasting sorghum genotypes, used in West Africa. Trials were carried out in a randomized complete blocks design with four replicates from 2013 to 2016 in Bambey, Sinthiou Malem and Nioro du Rip in Senegal. The results revealed three plant types. The first type, "biomass production", contained genotypes IS15401 and SK5912, and was linked to cycle duration, leaf area, and plant height. The second type, "grain production", grouped the caudatum race sorghum 621B, F2-20 and Soumba, and was associated with the number of grains per panicle and the width of the flag leaf. The third group, "dual-purpose", corresponding to the genotypes Fadda, Nieleni and Pablo, combined some favourable traits for grain and biomass: stem diameter, internode length, number of green leaves and number of grains per panicle. The study showed that high and stable grain yields were associated with stability in flag leaf size, phenology and number of grains per panicle, and a high and stable biomass yield was associated with stability in stem diameter. Those stable plant traits might be of interest for sorghum breeders selecting to develop dual-purpose varieties.

Modelling climate change impacts on maize yields under low nitrogen input conditions in sub-Saharan Africa.

Smallholder farmers in sub-Saharan Africa (SSA) currently grow rainfed maize with limited inputs including fertilizer. Climate change may exacerbate current production constraints. Crop models can help quantify the potential impact of climate change on maize yields, but a comprehensive multimodel assessment of simulation accuracy and uncertainty in these low-input systems is currently lacking. We evaluated the impact of varying [CO2 ], temperature and rainfall conditions on maize yield, for different nitrogen (N) inputs (0, 80, 160 kg N/ha) for five environments in SSA, including cool subhumid Ethiopia, cool semi-arid Rwanda, hot subhumid Ghana and hot semi-arid Mali and Benin using an ensemble of 25 maize models. Models were calibrated with measured grain yield, plant biomass, plant N, leaf area index, harvest index and in-season soil water content from 2-year experiments in each country to assess their ability to simulate observed yield. Simulated responses to climate change factors were explored and compared between models. Calibrated models reproduced measured grain yield variations well with average relative root mean square error of 26%, although uncertainty in model prediction was substantial (CV = 28%). Model ensembles gave greater accuracy than any model taken at random. Nitrogen fertilization controlled the response to variations in [CO2 ], temperature and rainfall. Without N fertilizer input, maize (a) benefited less from an increase in atmospheric [CO2 ]; (b) was less affected by higher temperature or decreasing rainfall; and (c) was more affected by increased rainfall because N leaching was more critical. The model intercomparison revealed that simulation of daily soil N supply and N leaching plays a crucial role in simulating climate change impacts for low-input systems. Climate change and N input interactions have strong implications for the design of robust adaptation approaches across SSA, because the impact of climate change in low input systems will be modified if farmers intensify maize production with balanced nutrient management.

Uncertainties in predicting rice yield by current crop models under a wide range of climatic conditions.

Predicting rice (Oryza sativa) productivity under future climates is important for global food security. Ecophysiological crop models in combination with climate model outputs are commonly used in yield prediction, but uncertainties associated with crop models remain largely unquantified. We evaluated 13 rice models against multi-year experimental yield data at four sites with diverse climatic conditions in Asia and examined whether different modeling approaches on major physiological processes attribute to the uncertainties of prediction to field measured yields and to the uncertainties of sensitivity to changes in temperature and CO2 concentration [CO2 ]. We also examined whether a use of an ensemble of crop models can reduce the uncertainties. Individual models did not consistently reproduce both experimental and regional yields well, and uncertainty was larger at the warmest and coolest sites. The variation in yield projections was larger among crop models than variation resulting from 16 global climate model-based scenarios. However, the mean of predictions of all crop models reproduced experimental data, with an uncertainty of less than 10% of measured yields. Using an ensemble of eight models calibrated only for phenology or five models calibrated in detail resulted in the uncertainty equivalent to that of the measured yield in well-controlled agronomic field experiments. Sensitivity analysis indicates the necessity to improve the accuracy in predicting both biomass and harvest index in response to increasing [CO2 ] and temperature.

How do various maize crop models vary in their responses to climate change factors?

Potential consequences of climate change on crop production can be studied using mechanistic crop simulation models. While a broad variety of maize simulation models exist, it is not known whether different models diverge on grain yield responses to changes in climatic factors, or whether they agree in their general trends related to phenology, growth, and yield. With the goal of analyzing the sensitivity of simulated yields to changes in temperature and atmospheric carbon dioxide concentrations [CO2 ], we present the largest maize crop model intercomparison to date, including 23 different models. These models were evaluated for four locations representing a wide range of maize production conditions in the world: Lusignan (France), Ames (USA), Rio Verde (Brazil) and Morogoro (Tanzania). While individual models differed considerably in absolute yield simulation at the four sites, an ensemble of a minimum number of models was able to simulate absolute yields accurately at the four sites even with low data for calibration, thus suggesting that using an ensemble of models has merit. Temperature increase had strong negative influence on modeled yield response of roughly -0.5 Mg ha(-1) per °C. Doubling [CO2 ] from 360 to 720 µmol mol(-1) increased grain yield by 7.5% on average across models and the sites. That would therefore make temperature the main factor altering maize yields at the end of this century. Furthermore, there was a large uncertainty in the yield response to [CO2 ] among models. Model responses to temperature and [CO2 ] did not differ whether models were simulated with low calibration information or, simulated with high level of calibration information.

Recombinant protein production by large-scale transient gene expression in mammalian cells: state of the art and future perspectives.

The expansion of the biologics pipeline depends on the identification of candidate proteins for clinical trials. Speed is one of the critical issues, and the rapid production of high quality, research-grade material for preclinical studies by transient gene expression (TGE) is addressing this factor in an impressive way: following DNA transfection, the production phase for TGE is usually 2-10 days. Recombinant proteins (r-proteins) produced by TGE can therefore enter the drug development and screening process in a very short time--weeks. With "classical" approaches to protein expression from mammalian cells, it takes months to establish a productive host cell line. This article summarizes efforts in industry and academia to use TGE to produce tens to hundreds of milligrams of r-proteins for either fundamental research or preclinical studies.

Targeting PIM kinases impairs survival of hematopoietic cells transformed by kinase inhibitor-sensitive and kinase inhibitor-resistant forms of Fms-like tyrosine kinase 3 and BCR/ABL.

Previous studies have shown that activation of the signal transducer and activator of transcription 5 (STAT5) plays an essential role in leukemogenesis mediated through constitutive activated protein tyrosine kinases (PTK). Because PIM-1 is a STAT5 target gene, we analyzed the role of the family of PIM serine/threonine kinases (PIM-1 to PIM-3) in PTK-mediated transformation of hematopoietic cells. Ba/F3 cells transformed to growth factor independence by various oncogenic PTKs (TEL/JAK2, TEL/TRKC, TEL/ABL, BCR/ABL, FLT3-ITD, and H4/PDGFbetaR) show abundant expression of PIM-1 and PIM-2. Suppression of PIM-1 activity had a negligible effect on transformation. In contrast, expression of kinase-dead PIM-2 mutant (PIM-2KD) led to a rapid decline of survival in Ba/F3 cells transformed by FLT3-ITD but not by other oncogenic PTKs tested. Coexpression of PIM-1KD and PIM-2KD abrogated growth factor-independent growth of Ba/F3 transformed by several PTKs, including BCR/ABL. Targeted down-regulation of PIM-2 by RNA interference (RNAi) selectively abrogated survival of Ba/F3 cells transformed by various Fms-like tyrosine kinase 3 (FLT3)-activating mutants [internal tandem duplication (ITD) and kinase domain] and attenuated growth of human cell lines containing FLT3 mutations. Interestingly, cells transformed by FLT3 and BCR/ABL mutations that confer resistance to small-molecule tyrosine kinase inhibitors were still sensitive to knockdown of PIM-2, or PIM-1 and PIM-2 by RNAi. Our observations indicate that combined inactivation of PIM-1 and PIM-2 interferes with oncogenic PTKs and suggest that PIMs are alternative therapeutic targets in PTK-mediated leukemia. Targeting the PIM kinase family could provide a new avenue to overcome resistance against small-molecule tyrosine kinase inhibitors.

Developmental cell death in dictyostelium does not require paracaspase.

Apoptotic cell death often requires caspases. Caspases are part of a family of related molecules including also paracaspases and metacaspases. Are molecules of this family generally involved in cell death? More specifically, do non-apoptotic caspase-independent types of cell death require paracaspases or metacaspases? Dictyostelium discoideum lends itself well to answering these questions because 1) it undergoes non-apoptotic developmental cell death of a vacuolar autophagic type and 2) it bears neither caspase nor metacaspase genes and apparently only one paracaspase gene. This only paracaspase gene can be inactivated by homologous recombination. Paracaspase-null clones were thus obtained in each of four distinct Dictyostelium strains. These clones were tested in two systems, developmental stalk cell death in vivo and vacuolar autophagic cell death in a monolayer system mimicking developmental cell death. Compared with parent cells, all of the paracaspase-null cells showed unaltered cell death in both test systems. In addition, paracaspase inactivation led to no alteration in development or interaction with a range of bacteria. Thus, in Dictyostelium, vacuolar programmed cell death in development and in a monolayer model in vitro would seem not to require paracaspase. To our knowledge, this is the first instance of developmental programmed cell death shown to be independent of any caspase, paracaspase or metacaspase. These results have implications as to the relationship in evolution between cell death and the caspase family.

Dictyostelium cell death: early emergence and demise of highly polarized paddle cells.

Cell death in the stalk of Dictyostelium discoideum, a prototypic vacuolar cell death, can be studied in vitro using cells differentiating as a monolayer. To identify early events, we examined potentially dying cells at a time when the classical signs of Dictyostelium cell death, such as heavy vacuolization and membrane lesions, were not yet apparent. We observed that most cells proceeded through a stereotyped series of differentiation stages, including the emergence of "paddle" cells showing high motility and strikingly marked subcellular compartmentalization with actin segregation. Paddle cell emergence and subsequent demise with paddle-to-round cell transition may be critical to the cell death process, as they were contemporary with irreversibility assessed through time-lapse videos and clonogenicity tests. Paddle cell demise was not related to formation of the cellulose shell because cells where the cellulose-synthase gene had been inactivated underwent death indistinguishable from that of parental cells. A major subcellular alteration at the paddle-to-round cell transition was the disappearance of F-actin. The Dictyostelium vacuolar cell death pathway thus does not require cellulose synthesis and includes early actin rearrangements (F-actin segregation, then depolymerization), contemporary with irreversibility, corresponding to the emergence and demise of highly polarized paddle cells.