Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize

XUECAI ZHANG Yunbi Xu Prasanna Boddupalli (2023)

Article

Pigment Accumulation Light Response CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ANTHOCYANINS LIGHT METABOLOMICS TRANSCRIPTOMICS WAXY MAIZE

Catching-up with genetic progress: Simulation of potential production for modern wheat cultivars in the Netherlands

João Vasco Silva Frits K. Van Evert Pytrik Reidsma (2023)

Context: Wheat crop growth models from all over the world have been calibrated on the Groot and Verberne (1991) data set, collected between 1982 and 1984 in the Netherlands, in at least 28 published studies to date including various recent ones. However, the recent use of this data set for calibration of potential yield is questionable as actual Dutch winter wheat yields increased by 3.1 Mg ha-1 over the period 1984 – 2015. A new comprehensive set of winter wheat experiments, suitable for crop model calibration, was conducted in Wageningen during the growing seasons of 2013–2014 and of 2014–2015. Objective: The present study aimed to quantify the change of winter wheat variety traits between 1984 and 2015 and to examine which of the identified traits explained the increase in wheat yield most. Methods: PCSE-LINTUL3 was calibrated on the Groot and Verberne data (1991) set. Next, it was evaluated on the 2013–2015 data set. The model was further recalibrated on the 2013–2015 data set. Parameter values of both calibrations were compared. Sensitivity analysis was used to assess to what extent climate change, elevated CO2, changes in sowing dates, and changes in cultivar traits could explain yield increases. Results: The estimated reference light use efficiency and the temperature sum from anthesis to maturity were higher in 2013–2015 than in 1982–1984. PCSE-LINTUL3, calibrated on the 1982–1984 data set, underestimated the yield potential of 2013–2015. Sensitivity analyses showed that about half of the simulated winter wheat yield increase between 1984 and 2015 in the Netherlands was explained by elevated CO2 and climate change. The remaining part was explained by the increased temperature sum from anthesis to maturity and, to a smaller extent, by changes in the reference light use efficiency. Changes in sowing dates, biomass partitioning fractions, thermal requirements for anthesis, and biomass reallocation did not explain the yield increase. Conclusion: Recalibration of PCSE-LINTUL3 was necessary to reproduce the high wheat yields currently obtained in the Netherlands. About half of the reported winter wheat yield increase was attributed to climate change and elevated CO2. The remaining part of the increase was attributed to changes in the temperature sum from anthesis to maturity and, to a lesser extent, the reference light use efficiency. Significance: This study systematically addressed to what extent changes in various cultivar traits, climate change, and elevated CO2 can explain the winter wheat yield increase observed in the Netherlands between 1984 and 2015.

Article

Light Use Efficiency Potential Yield CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CROP MODELLING LIGHT PHENOLOGY MAXIMUM SUSTAINABLE YIELD TRITICUM AESTIVUM WINTER WHEAT

Carbamazepine degradation by visible-light-driven photocatalyst Ag3PO4/GO: Mechanism and pathway

Guanhan Chen Wenyi Dong Hongjie Wang Zilong Zhao Feng Wang Feifei Wang César Nieto Delgado (2022)

"Carbamazepine (CBZ), as one of the most frequently detected pharmaceuticals, is of great concern due to its potential impact on the ecosystem and human health. This study provides an effective approach to remove CBZ by using photocatalyst silver phosphate combined with graphene oxide (Ag3PO4/GO) under visible irradiation. The morphology, composition, and optical properties of Ag3PO4/GO were characterized employing SEM, XRD, and DRS. Graphene oxide could improve the visible-light utilization and promote electron's charge to enhance the photocatalytic performance of Ag3PO4/GO. With the optimal reaction condition of 5.86 mW/cm(2) light intensity, 15-25 degrees C temperature, 5-7 pH, and 0.5 mg/L catalytic dosages, 5 mg/L CBZ could be completely degraded in 30 min, and the apparent rate constant could reach 0.12 min(-1). Additionally, the radical trapping experiments indicated center dot OH and O-2(-)center dot were the main reactive oxygen species employed to eliminate CBZ. The decay pathways of CBZ had been proposed accordingly, and the main product was the low-molecular products. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Chinese Society for Environmental Sciences, Harbin Institute of Technology, Chinese Research Academy of Environmental Sciences."

Article

Carbamazepine Ag3PO4/GO Visible light Photocatalysis INGENIERÍA Y TECNOLOGÍA INGENIERÍA Y TECNOLOGÍA

GENERATION OF LG VECTOR MODES WITH ULTRAHIGH STABILITY BASED ON COMPLEX AMPLITUDE MODULATION IN AN ON-AXIS CONFIGURATION

Gloria Elizabth Rodríguez García (2023)

"This thesis presents a novel technique for generating vector beams using complex amplitude modulation (CAM) in an on-axis configuration. The holograms used to generate the beams were created using the Mathlab software and displayed on a reflective spatial light modulator (SLM). The main goal of this research was to address both the purity and stability of the beams during generation and propagation, introducing a quantitative approach to assess their stability. As a proof-of-concept, Laguerre-Gaussian vector beams have been generated and characterized using Stokes polarimetry with the proposed experimental set up."

Master thesis

Structured light Laguerre-Gauss vector beams Stokes polarimetry Beam generation Spatial light modulators CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA FÍSICA ÓPTICA OPTICA FÍSICA OPTICA FÍSICA

Does access to improved grain storage technology increase farmers' welfare? Experimental evidence from maize farming in Ethiopia

Hugo De Groote Bart Minten (2024)

Seasonal price variability for cereals is two to three times higher in Africa than on the international reference market. Seasonality is even more pronounced when access to appropriate storage and opportunities for price arbitrage are limited. As smallholder farmers typically sell their production after harvest, when prices are low, this leads to lower incomes as well as higher food insecurity during the lean season, when prices are high. One solution to reduce seasonal stress is the use of improved storage technologies. Using data from a randomised controlled trial, in a major maize-growing region of Western Ethiopia, we study the impact of hermetic bags, a technology that protects stored grain against insect pests, so that the grain can be stored longer. Despite considerable price seasonality—maize prices in the lean season are 36% higher than after harvesting—we find no evidence that hermetic bags improve welfare, except that access to these bags allowed for a marginally longer storage period of maize intended for sale by 2 weeks. But this did not translate into measurable welfare gains as we found no changes in any of our welfare outcome indicators. This ‘near-null’ effect is due to the fact that maize storage losses in our study region are relatively lower than previous studies suggested—around 10% of the quantity stored—likely because of the widespread use of an alternative to protect maize during storage, for example a cheap but highly toxic fumigant. These findings are important for policies that seek to promote improved storage technologies in these settings.

Article

Hermetic Storage Randomised Controlled Trial CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA STORAGE PILOT FARMS SEASONALITY WELFARE MAIZE

Sustainable maize intensification through site-specific nutrient management advice: Experimental evidence from Nigeria

Miet Maertens Oyakhilomen Oyinbo Tahirou Abdoulaye Jordan Chamberlin (2023)

There is growing evidence on the impacts of site-specific nutrient management (SSNM) from Asia. The evidence for Sub-Saharan Africa (SSA), where SSNM developments are more recent and where conditions concerning soil fertility and fertilizer use differ importantly from those in Asia, is extremely scarce. We evaluate a SSNM advisory tool that allows extension agents to generate fertilizer recommendations tailored to the specific situation of an individual farmer’s field, using a three-year randomized controlled trial with 792 smallholder farmers in the maize belt of northern Nigeria. Two treatment arms were implemented: T1 and T2 both provide SSNM information on nutrient use and management, but T2 provides additional information on maize price distributions and the associated variability of expected returns to fertilizer use. We estimate average and heterogenous intent-to-treat effects on agronomic, economic and environmental plot-level outcomes. We find that T1 and T2 lead to substantial increases (up to 116%) in the adoption of good fertilizer management practices and T2 leads to incremental increases (up to 18%) in nutrient application rates, yields and revenues. Both treatments improve low levels of nutrient use efficiency and reduce high levels of greenhouse gas emission intensity, after two years of treatment. Our findings underscore the possibility of a more gradual and sustainable intensification of smallholder agriculture in SSA, as compared with the Asian Green Revolution, through increased fertilizer use accompanied by improved fertilizer management.

Article

Randomized Controlled Trial CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA TECHNOLOGY ADOPTION AGRICULTURAL EXTENSION GREEN REVOLUTION FERTILIZERS GREENHOUSE GAS EMISSIONS

A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations

David Israel Flores Granados (2014)

The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. © 2014 Flores et al.

Article

1UU9 protein, 3HRC protein, protein, thymidylate synthase, unclassified drug, protein kinase, thymidylate synthase, accuracy, algorithm, Article, CMASA, CMASA Substitution Matrix, Contact Matrix Average Deviation, controlled study, correlation coeffi CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA MATEMÁTICAS ANÁLISIS NUMÉRICO ANÁLISIS NUMÉRICO

Assessing the Response of Nematode Communities to Climate Change-Driven Warming: A Microcosm Experiment

RUTH GINGOLD WERMUTH (2013)

Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for alternative diversity-ecosystem functioning relationships, such as the Rivets and the Idiosyncrasy Model. © 2013 Gingold et al.

Article

aquaculture, article, bacterivore, benthos, biodiversity, biomass, climate, community dynamics, controlled study, ecosystem, environmental temperature, microcosm, nematode, nonhuman, population abundance, species diversity, species richness, taxonomy CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019)

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Maintenance of Coastal Surface Blooms by Surface Temperature Stratification and Wind Drift

MARY CARMEN RUIZ DE LA TORRE (2013)

Algae blooms are an increasingly recurrent phenomenon of potentially socio-economic impact in coastal waters globally and in the coastal upwelling region off northern Baja California, Mexico. In coastal upwelling areas the diurnal wind pattern is directed towards the coast during the day. We regularly found positive Near Surface Temperature Stratification (NSTS), the resulting density stratification is expected to reduce the frictional coupling of the surface layer from deeper waters and allow for its more efficient wind transport. We propose that the net transport of the top layer of approximately 2.7 kilometers per day towards the coast helps maintain surface blooms of slow growing dinoflagellate such as Lingulodinium polyedrum. We measured: near surface stratification with a free-rising CTD profiler, trajectories of drifter buoys with attached thermographs, wind speed and direction, velocity profiles via an Acoustic Doppler Current Profiler, Chlorophyll and cell concentration from water samples and vertical migration using sediment traps. The ADCP and drifter data agree and show noticeable current shear within the first meters of the surface where temperature stratification and high cell densities of L. polyedrum were found during the day. Drifters with 1m depth drogue moved towards the shore, whereas drifters at 3 and 5 m depth showed trajectories parallel or away from shore. A small part of the surface population migrated down to the sea floor during night thus reducing horizontal dispersion. The persistent transport of the surface bloom population towards shore should help maintain the bloom in favorable environmental conditions with high nutrients, but also increasing the potential socioeconomic impact of the blooms. The coast wise transport is not limited to blooms but includes all dissolved and particulate constituents in surface waters. © 2013 Ruiz-de la Torre et al.

Article

chlorophyll, algal bloom, article, cell count, cell density, coastal waters, controlled study, dinoflagellate, Lingulodinium polyedrum, meteorological phenomena, Mexico, near surface temperature stratification, nonhuman, nutrient concentration, popul CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA