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Horticulture Research Jun 2024Cupressaceae is a conifer family rich in plants of horticultural importance, including , , , and , yet genomic surveys are lacking for this family. , one of the many...
Cupressaceae is a conifer family rich in plants of horticultural importance, including , , , and , yet genomic surveys are lacking for this family. , one of the many rare conifers that are threatened by climate change and anthropogenic habitat fragmentation, plays an ever-increasing role in ecotourism in Tibet. To infer how past climate change has shaped the population evolution of this species, we generated a chromosome-scale genome (10.92 Gb) and compared the species' population history and genetic load with that of a widespread close relative, . Our demographic analyses, based on 83 re-sequenced individuals from multiple populations of the two species, revealed a sharp decline of population sizes during the first part of the Quaternary. However, populations of then started to recover, while populations continued to decrease until recently. The total genomic diversity of is smaller than that of , but contrary to expectations, has fewer highly and mildly deleterious mutations than , and simulations and statistical tests support purifying selection during prolonged inbreeding as the explanation. Our results highlight the evolutionary consequences of decreased population size on the genetic burden of a long-lived endangered conifer with large genome size and suggest that genetic purging deserves more attention in conservation management.
PubMed: 38883334
DOI: 10.1093/hr/uhae108 -
Journal of Pharmacy & Bioallied Sciences Apr 2024The metabolism of glucose is carefully regulated by several chemical elements and plays a critical part in preserving cellular energy balance. Our study investigates...
AIM
The metabolism of glucose is carefully regulated by several chemical elements and plays a critical part in preserving cellular energy balance. Our study investigates possible connections between the essential proteins CYTIP, C1QL3, and CYBB, which are involved in the metabolism of glucose, and pelargonidin, a naturally occurring plant chemical. The underlying mechanisms of pelargonidin's anti-diabetic effects are still unknown.
MATERIALS AND METHODS
We examine the binding affinities and possible binding sites between pelargonidin and C1QL3/CYBB AND CYTIP using molecular docking simulations. The results demonstrate favorable docking scores and potential binding sites, suggesting the formation of stable complexes between pelargonidin and the target proteins.
RESULTS
This finding means that pelargonidin may modulate the function of C1QL3 and CYBB, CYTIP consequently influencing glucose metabolism.
CONCLUSION
This study provides a foundation for future experimental investigations to validate the predicted interactions and explore the mechanisms through which pelargonidin affects glucose metabolism. Understanding these molecular interactions could lead to the development of new therapeutic strategies for glucose metabolism and its related disorders.
PubMed: 38882825
DOI: 10.4103/jpbs.jpbs_590_23 -
Nature Communications Jun 2024Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene...
Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.
Topics: Arabidopsis Proteins; Arabidopsis; Introns; Gene Expression Regulation, Plant; Spliceosomes; Light; Ubiquitin-Protein Ligases; Cell Nucleus; Seedlings; Alternative Splicing; Ubiquitination
PubMed: 38879536
DOI: 10.1038/s41467-024-49571-9 -
Plant Methods Jun 2024Image-based crop growth modeling can substantially contribute to precision agriculture by revealing spatial crop development over time, which allows an early and...
BACKGROUND
Image-based crop growth modeling can substantially contribute to precision agriculture by revealing spatial crop development over time, which allows an early and location-specific estimation of relevant future plant traits, such as leaf area or biomass. A prerequisite for realistic and sharp crop image generation is the integration of multiple growth-influencing conditions in a model, such as an image of an initial growth stage, the associated growth time, and further information about the field treatment. While image-based models provide more flexibility for crop growth modeling than process-based models, there is still a significant research gap in the comprehensive integration of various growth-influencing conditions. Further exploration and investigation are needed to address this gap.
METHODS
We present a two-stage framework consisting first of an image generation model and second of a growth estimation model, independently trained. The image generation model is a conditional Wasserstein generative adversarial network (CWGAN). In the generator of this model, conditional batch normalization (CBN) is used to integrate conditions of different types along with the input image. This allows the model to generate time-varying artificial images dependent on multiple influencing factors. These images are used by the second part of the framework for plant phenotyping by deriving plant-specific traits and comparing them with those of non-artificial (real) reference images. In addition, image quality is evaluated using multi-scale structural similarity (MS-SSIM), learned perceptual image patch similarity (LPIPS), and Fréchet inception distance (FID). During inference, the framework allows image generation for any combination of conditions used in training; we call this generation data-driven crop growth simulation.
RESULTS
Experiments are performed on three datasets of different complexity. These datasets include the laboratory plant Arabidopsis thaliana (Arabidopsis) and crops grown under real field conditions, namely cauliflower (GrowliFlower) and crop mixtures consisting of faba bean and spring wheat (MixedCrop). In all cases, the framework allows realistic, sharp image generations with a slight loss of quality from short-term to long-term predictions. For MixedCrop grown under varying treatments (different cultivars, sowing densities), the results show that adding these treatment information increases the generation quality and phenotyping accuracy measured by the estimated biomass. Simulations of varying growth-influencing conditions performed with the trained framework provide valuable insights into how such factors relate to crop appearances, which is particularly useful in complex, less explored crop mixture systems. Further results show that adding process-based simulated biomass as a condition increases the accuracy of the derived phenotypic traits from the predicted images. This demonstrates the potential of our framework to serve as an interface between a data-driven and a process-based crop growth model.
CONCLUSION
The realistic generation and simulation of future plant appearances is adequately feasible by multi-conditional CWGAN. The presented framework complements process-based models and overcomes their limitations, such as the reliance on assumptions and the low exact field-localization specificity, by realistic visualizations of the spatial crop development that directly lead to a high explainability of the model predictions.
PubMed: 38879522
DOI: 10.1186/s13007-024-01205-3 -
Journal of Thermal Biology May 2024Life history traits have been studied under various environmental factors, but the ability to combine them into a simple function to assess pest response to climate is...
Life history traits have been studied under various environmental factors, but the ability to combine them into a simple function to assess pest response to climate is still lacking complete understanding. This study proposed a risk index derived by combining development, mortality, and fertility rates from a stage-structured dynamic mathematical model. The first part presents the theoretical framework behind the risk index. The second part of the study is concerned with the application of the index in two case studies of major economic pest: the brown planthopper (Nilaparvata lugens) and the spotted wing drosophila (Drosophila suzukii), pests of rice crops and soft fruits, respectively. The mathematical calculations provided a single function composed of the main thermal biodemographic rates. This function has a threshold value that determines the possibility of population increase as a function of temperature. The tests carried out on the two pest species showed the capability of the index to describe the range of favourable conditions. With this approach, we were able to identify areas where pests are tolerant to climatic conditions and to project them on a geospatial risk map. The theoretical background developed here provided a tool for understanding the biogeography of Nilaparvata lugens and Drosophila suzukii. It is flexible enough to deal with mathematically simple (N. lugens) and complex (D. Suzukii) case studies of crop insect pests. It produces biologically sound indices that behave like thermal performance curves. These theoretical results also provide a reasonable basis for addressing the challenge of pest management in the context of seasonal weather variations and climate change. This may help to improve monitoring and design management strategies to limit the spread of pests in invaded areas, as some non-invaded areas may be suitable for the species to develop.
Topics: Animals; Hemiptera; Drosophila; Temperature; Risk Assessment; Models, Biological
PubMed: 38878392
DOI: 10.1016/j.jtherbio.2024.103886 -
Molecular Plant Jun 2024Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory...
Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. We identified 16 diverse gene clusters with differential spatiotemporal expression patterns and revealed biased regulation of redox, programmed cell death, and hormone signals during meristem differentiation between ear and tassel. Notably, based on their dynamic expression patterns, we revealed the roles of two RNA-binding proteins in regulating inflorescence meristem activity and axillary meristem formation. Moreover, using the transcriptional profiles of 53 910 single cells, we uncovered the cellular heterogeneity between ear and tassel florets. We found that multiple signals associated with either enhanced cell death or reduced growth are responsible for tassel pistil suppression, while part of the gibberellic acid signal may act non-cell-autonomously to regulate ear stamen arrest during sex differentiation. We further showed that the pistil-protection gene SILKLESS 1 (SK1) functions antagonistically to the known pistil-suppression genes through regulating common molecular pathways, and constructed a regulatory network for pistil-fate determination. Collectively, our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation for identifying new regulators and pathways for maize hybrid breeding and improvement.
PubMed: 38877701
DOI: 10.1016/j.molp.2024.06.007 -
Frontiers in Plant Science 2024The resistance of to clubroot, a major disease of Brassicaceae caused by the obligate protist , is controlled in part by epigenetic factors. The detection of some of...
The resistance of to clubroot, a major disease of Brassicaceae caused by the obligate protist , is controlled in part by epigenetic factors. The detection of some of these epigenetic quantitative trait loci (QTL) has been shown to depend on experimental conditions. The aim of the present study was to assess whether and how temperature and/or soil water availability influenced both the detection and the extent of the effect of response QTL. The epigenetic recombinant inbred line (epiRIL) population, derived from the cross between and Col-0 (partially resistant and susceptible to clubroot, respectively), was phenotyped for response to under four abiotic conditions including standard conditions, a 5°C temperature increase, drought, and flooding. The abiotic constraints tested had a significant impact on both the leaf growth of the epiRIL population and the outcome of the epiRIL-pathogen interaction. Linkage analysis led to the detection of a total of 31 QTL, 18 of which were specific to one abiotic condition and 13 common to at least two environments. EpiRIL showed significant plasticity under epigenetic control, which appeared to be specific to the traits evaluated and to the abiotic conditions. These results highlight that the environment can affect the epigenetic architecture of plant growth and immune responses and advance our understanding of the epigenetic factors underlying plasticity in response to climate change.
PubMed: 38872892
DOI: 10.3389/fpls.2024.1245545 -
Journal of Arthropod-borne Diseases Dec 2023Kerman Province is one of the endemic foci of scorpionism in southeastern Iran. Totally 17 species are reported for Kerman Province fauna. The current study seeks to...
BACKGROUND
Kerman Province is one of the endemic foci of scorpionism in southeastern Iran. Totally 17 species are reported for Kerman Province fauna. The current study seeks to determine the fauna of medically important scorpions in northern parts of this province.
METHODS
A descriptive cross-sectional study was conducted from January 2019 to March 2021. The specimens were captured from different areas, by rock-rolling during day and using Ultraviolet light at night. The specimens were preserved in ethanol (80%) and then identified using reliable identification keys for scorpions.
RESULTS
Totally, 499 specimens were captured from eight cities in northern Kerman. In total, 11 species belonging to three families were identified. sp. is reported for the first time from Kerman Province. sp., cf. , and cf. , were the lowest in frequency of occurrence, against as the highest frequency.
CONCLUSION
The results of this study are useful for the preparation of regional or monovalent antivenom for the Razi Vaccine and Serum Research Institute. Additionally, the obtained data are useful for the effective planning of scorpion control programs in the northern parts of Kerman Province, Iran.
PubMed: 38868675
DOI: 10.18502/jad.v17i4.15295 -
Journal of Animal Science and... Jun 2024Weaning stress reduces growth performance and health of young pigs due in part to an abrupt change in diets from highly digestible milk to fibrous plant-based...
Prebiotic galactooligosaccharide improves piglet growth performance and intestinal health associated with alterations of the hindgut microbiota during the peri-weaning period.
BACKGROUND
Weaning stress reduces growth performance and health of young pigs due in part to an abrupt change in diets from highly digestible milk to fibrous plant-based feedstuffs. This study investigated whether dietary galactooligosaccharide (GOS), supplemented both pre- and post-weaning, could improve growth performance and intestinal health via alterations in the hindgut microbial community.
METHODS
Using a 3 × 2 factorial design, during farrowing 288 piglets from 24 litters received either no creep feed (FC), creep without GOS (FG-) or creep with 5% GOS (FG+) followed by a phase 1 nursery diet without (NG-) or with 3.8% GOS (NG+). Pigs were sampled pre- (D22) and post-weaning (D31) to assess intestinal measures.
RESULTS
Creep fed pigs grew 19% faster than controls (P < 0.01) prior to weaning, and by the end of the nursery phase (D58), pigs fed GOS pre-farrowing (FG+) were 1.85 kg heavier than controls (P < 0.05). Furthermore, pigs fed GOS in phase 1 of the nursery grew 34% faster (P < 0.04), with greater feed intake and efficiency. Cecal microbial communities clustered distinctly in pre- vs. post-weaned pigs, based on principal coordinate analysis (P < 0.01). No effects of GOS were detected pre-weaning, but gruel creep feeding increased Chao1 α-diversity and altered several genera in the cecal microbiota (P < 0.05). Post-weaning, GOS supplementation increased some genera such as Fusicatenibacter and Collinsella, whereas others decreased such as Campylobacter and Frisingicoccus (P < 0.05). Changes were accompanied by higher molar proportions of butyrate in the cecum of GOS-fed pigs (P < 0.05).
CONCLUSIONS
Gruel creep feeding effectively improves suckling pig growth regardless of GOS treatment. When supplemented post-weaning, prebiotic GOS improves piglet growth performance associated with changes in hindgut microbial composition.
PubMed: 38867260
DOI: 10.1186/s40104-024-01047-y -
European Journal of Pharmaceutical... Jun 2024The separation and purification of plant-based Active Pharmaceutical Ingredients (API) from extracts is a crucial part in pharmaceutical process development. For the...
The separation and purification of plant-based Active Pharmaceutical Ingredients (API) from extracts is a crucial part in pharmaceutical process development. For the purification of the antimalarial drug component artemisinin (ARTE) from an Artemisia anna L. toluene extract, antisolvent crystallization is considered. Solubilities of ARTE in binary solvent mixtures of toluene and two potential antisolvents, n-heptane and ethanol, were determined at temperatures from 278.15 K to 313.15 K. The experimental work was supported by the application of various models, utilizing varying amounts of experimental input data. The goal was the identification of models that are able to predict solubilities in binary solvent mixtures sufficiently accurate and, thus, can help to reduce the experimental effort for future solvent screenings. In this study, we applied the PC-SAFT model both with and without fitting the binary interaction parameter k between ARTE and the respective solvent, as well as the empirical Jouyban-Acree model. From the experiments, n-heptane demonstrated to be a promising antisolvent, while ethanol acted more as a cosolvent. All models tested were capable of distinguishing between effective and ineffective antisolvents. The purely predictive PC-SAFT model applied with k = 0 exhibited the largest deviation from the experimental data. This was followed by the PC-SAFT model including fitted k values, based on at least four experimental data points. The Jouyban-Acree model fitted the data most accurately. Its parametrization required a minimum of ten experimental data points.
PubMed: 38866112
DOI: 10.1016/j.ejps.2024.106826