Natural Variation Research Articles

Distribution of cool starspots on the surface of the red dwarf V647 Her

Photometric observations of the star V647 Her (M3.5V) obtained in 2022 at the 1.25 m telescope of the Crimean Astrophysical Observatory are analyzed. The presence of a low-amplitude variability in brightness of the star with a period of 20.69 d, found from observations in 2019, is confirmed; it is shown that as the brightness decreases, the star becomes redder. The observed nature of photometric variability is due to the presence of cool spots on the surface of the star and manifestation of rotational brightness modulation with a full amplitude of no more than 0m.05. We have performed a comparison of the photometric results obtained in 2019, 2022 and 2004. The zones of starspot concentrations in different epochs were determined from the analysis of phase curves. The distribution of spots has been maintained for 40–100 days. Starspot parameters were estimated in the framework of the zonal model. The temperature of the spots is 2700–2800 K. The area they occupied in 2004 is 15% of the total surface area of the star. According to the 2019 and 2022 data, it increases to 30%. The difference between the spottedness of the hemispheres caused by their seasonal redistribution is less than 2%.

Natural variation in the adjustment of primary metabolism determines ammonium tolerance in the model grass Brachypodium distachyon.

Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. In this work, we studied Brachypodium distachyon, the model plant for C3 grasses, grown with NH4+ or NO3- supply. We performed gene expression analysis in the root of the B. distachyon reference accession Bd21 and examined the phenotypic variation across 52 natural accessions through analysing plant growth and a panel of 22 metabolic traits in leaf and root. We found that the adjustment of primary metabolism to ammonium nutrition is essential for the natural variation of NH4+ tolerance, notably involving NH4+ assimilation and PEPC activity. Additionally, genome-wide association studies (GWAS) indicated several loci associated with B. distachyon growth and metabolic adaptation to NH4+ nutrition. For instance, we found that the GDH2 gene was associated with the induction of root GDH activity under NH4+ nutrition and that two genes encoding malic enzyme were associated with leaf PEPC activity. Altogether, our work underlines the value of natural variation and the key role of primary metabolism to improve NH4+ tolerance.

Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures.

Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types-to 'map' variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal ( https://g2p.broadinstitute.org/ ): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotypes.

Recent heatwaves as a prelude to climate extremes in the western Mediterranean region

The 2022 and 2023 western Mediterranean summer temperatures exceeded millennial natural variability, reaching unprecedented anomalies of +3.6 °C and +2.9 °C respectively. We show that anthropogenic climate change may turn extreme heatwaves from a rarity of 1 in 10,000 years into events occurring every 4–75 years, depending on future scenarios. This shift underscores the urgency of implementing adaptive strategies as extreme climate events manifest sooner and more intensely than expected.

Iterative LMI-Tuned PID Controller for Robust Decentralized Multi-Area Automatic Generation Control in Deregulated Electricity Markets

This study proposes an Iterative Linear Matrix Inequality (LMI)-Tuned Proportional-Integral-Derivative (PID) controller for robust decentralized AGC in the context of deregulated electricity markets. The study addresses the challenges posed by market uncertainties and diverse generation sources, aiming to enhance the stability and performance of power systems. This study is driven by the urgent need to develop robust AGC strategies that are adapted to the complex dynamics of decentralized power systems operating in deregulated markets. The conventional centralized control approaches are often inadequate to address the diverse and distributed nature of modern generation units. Furthermore, the intermittent and variable nature of renewable energy sources adds a layer of complexity that demands innovative control solutions. The impact of bilateral contracts on the dynamics is taken into consideration while modifying the conventional LFC of interconnected power networks. To model these bilateral contracts, the distribution company (DISCO) participation matrix (DPM) is presented, and the multi-area block diagram reflects these concepts. Simulation studies are conducted to evaluate and compare the performance of the proposed Iterative LMI-Tuned PID Controller and Conventional PID Controller. Results are analyzed against key performance metrics, considering scenarios reflective of diverse market conditions. Comparative studies with the conventional PID controller provide insights into the efficacy and robustness of the proposed approach.

The impact of light adjustment versus tuneable white mode on ICU staff’s circadian rhythms

ABSTRACT The significance of lighting design in intensive care units (ICUs) for healthcare professionals’ demanding work and its profound impact on health, visual comfort and overall well-being cannot be overstated. This study investigates the potential of controlling luminous flux and spectral characteristics to enhance ICU lighting environments. It aims to determine whether modifying the lighting spectrum positively affects health without compromising visual comfort and colour discrimination. Two distinct LED lighting configurations were tested. The first adjusted only light levels, providing insights into staff responses. The second used tuneable white lighting, allowing changes in spectral content and colour temperature throughout shifts, resembling natural light variations. Effects were assessed via subjective perception surveys and objective colour rendering tests. Physiological impacts were evaluated through urine and blood samples, analysing melatonin suppression and cortisol levels, crucial for regulating rhythms and stress. Results offer valuable insights into lighting’s impact on ICU occupants’ well-being, highlighting the potential benefits of spectral adjustments while maintaining visual comfort and colour discrimination. This holistic approach to lighting design in critical care settings emphasizes the importance of balancing health benefits with lighting quality.

Thermal and morphometric correlates of the extremely low rate of energy use in a wild frugivorous primate, the Mayotte lemur

Primates spend on average half as much energy as other placental mammals while expressing a wide range of lifestyles. However, little is known about how primates adapt their rate of energy use in the context of natural environmental variations. Using doubly labelled water, behavioral and accelerometric methods, we measured the total energy expenditure (TEE) and body composition of a population of Eulemur fulvus (N = 12) living in an agroforest in Mayotte. We show that the TEE of this medium-sized cathemeral primate is one of the lowest recorded to date in eutherians. Regression models show that individual variation in the rate of energy use is predicted by fat-free mass, body size, thigh thickness and maximum temperature. TEE is positively correlated with increasing temperature, suggesting that thermoregulation is an important component of the energy budget of this frugivorous species. Mass-specific TEE is only 10% lower than that of a closely related species previously studied in a gallery forest, consistent with the assertion that TEE varies within narrow physiological limits. As lemur communities include many species with unique thermoregulatory adaptations, circadian and/or seasonal temperature variations may have constituted a major selective pressure on the evolution of lemur metabolic strategies.

Natural variations in the Cis-elements of GhRPRS1 contributing to petal colour diversity in cotton.

The cotton genus comprises both diploid and allotetraploid species, and the diversity in petal colour within this genus offers valuable targets for studying orthologous gene function differentiation and evolution. However, the genetic basis for this diversity in petal colour remains largely unknown. The red petal colour primarily comes from C, G, K, and D genome species, and it is likely that the common ancestor of cotton had red petals. Here, by employing a clone mapping strategy, we mapped the red petal trait to a specific region on chromosome A07 in upland cotton. Genomic comparisons and phylogenetic analyses revealed that the red petal phenotype introgressed from G. bickii. Transcriptome analysis indicated that GhRPRS1, which encodes a glutathione S-transferase, was the causative gene for the red petal colour. Knocking out GhRPRS1 resulted in white petals and the absence of red spots, while overexpression of both genotypes of GhRPRS1 led to red petals. Further analysis suggested that GhRPRS1 played a role in transporting pelargonidin-3-O-glucoside and cyanidin-3-O-glucoside. Promoter activity analysis indicated that variations in the promoter, but not in the gene body of GhRPRS1, have led to different petal colours within the genus. Our findings provide new insights into orthologous gene evolution as well as new strategies for modifying promoters in cotton breeding.

The responsiveness of rural poverty to structural and rural transformations in Ethiopia

AbstractThis study investigates the effects of economic opportunities created by structural transformation, such as income from labor employment and income from nonlabor sources, on the incidence, depth, and severity of rural poverty using the 2018/2019 Ethiopian Socioeconomic Survey data. The effects of rural transformations in terms of nonfarm self‐employment and improved farming systems on poverty are also investigated. Ordinary least square, Probit, Instrumental Variable Probit model, and two stage least square estimation methods are used depending on the nature of outcome variables and the Wald test of exogeneity. The findings show that labor income (especially regular salaried income) and nonlabor income (especially remittance from international sources) are crucial in reducing the incidence of rural poverty. Improvements in crop and livestock practices, on the other hand, reduce the incidence as well as depth and severity of rural poverty. The findings suggest that more attention should be given to enhancing the modernization of crop and livestock sectors by expanding access to farm credit and improved extension systems, among other things.

Characterization, quantitation, and natural variability of phenolics in Rhododendron arboreum leaves of western Himalayan origin using UPLC-PDA and UHPLC-ESI-Q/TOF-MS/MS

Rhododendron arboreum Sm. is very popular in the Indian Himalayan region due to its significant ethnomedicinal importance and potential commercial applications. Apart from the ornamental value derived from its vibrant red flowers, fresh flowers are used to prepare medicinal juices, and dried are utilized as spices. Despite being a rich source of phenolics, these lack identified marker chemicals and validated methods. The present work encompasses the chemical investigation of R. arboreum leaves using UHPLC-ESI-Q/TOF-MS/MS. The chemotypic variability was assessed through a reverse phase ultra-performance liquid chromatography method coupled with a photodiode array detector (RP-UPLC-PDA) chemical signatures of R. arboreum leaves from different altitudes combined with chemometric analysis. The chromatographic method was developed and validated for the quantitative analysis of three vital secondary metabolites, i.e., Isoquercetin or Quercetin-3-O-glucoside (Qg), Reynoutrin or Quercetin-3-O-xyloside (Qx), and Quercitrin or Quercetin-3-O-rhamnoside (Qr)The hyphenation of the method with ESI-Q/TOF-MS/MS has confirmed the distribution of 11 chemicals (nine known and two unknown) in R. arboreum leaves belonging to the phenolic and hydrolyzable tannins class. Samples from higher altitudes >3000 m (above mean sea level) were exceptionally rich in Quercitrin. The chemometric investigation, comprising hierarchical cluster analysis (HCA), principal component analysis (PCA), and partial least square method-discriminant analysis (PLS-DA), successfully categorized thirty-three samples from diverse geographic regions into two distinct categories. This current study provides a validated method for the chemotypic discrimination and quality assessment of the R. arboreum leaves from Uttarakhand, Western Himalayan region of India, and laid the foundation for the comprehensive utilization of these renewable and sustainable resources.

EMS-induced missense mutation in TaCHLI-7D affects leaf color and yield-related traits in wheat.

Mutations in TaCHLI impact chlorophyll levels and yield-related traits in wheat. Natural variations in TaCHLI-7A/B influence plant productivity, offering potential for molecular breeding. Chlorophyll is essential for plant growth and productivity. The CHLI subunit of the magnesium chelatase protein plays a key role inserting magnesium into protoporphyrin IX during chlorophyll biosynthesis. Here, we identify a novel wheat mutant chlorophyll (chl) that exhibits yellow-green leaves, reduced chlorophyll levels, and increased carotenoid content, leading to an overall decline in yield-related traits. Map-based cloning reveals that the chl phenotype is caused by a point mutation (Asp186Asn) in the TaCHLI-7D gene, which encodes subunit I of magnesium chelatase. Furthermore, the three TaCHLI mutants: chl-7b-1 (Pro82Ser), chl-7b-2 (Ala291Thr), and chl-7d-1 (Gly357Glu), also showed significant reductions in chlorophyll content and yield-related traits. However, TaCHLI-7D overexpression in rice significantly decreased thousand kernel weight, yield per plant, and germination. Additionally, natural variations in TaCHLI-7A/B are significantly associated with flag leaf, spike exsertion length, and yield per plant. Notably, the favorable haplotype, TaCHLI-7B-HapII, which displayed higher thousand kernel weight and yield per plant, is positively selected in wheat breeding. Our study provides insights on the regulatory molecular mechanisms underpinning leaf color and chlorophyll biosynthesis, and highlights TaCHLI functions, which provide useful molecular markers and genetic resources for wheat breeding.

Features of Temporal Variability of the Concentrations of Gaseous Trace Pollutants in the Air of the Urban and Rural Areas in the Southern Baikal Region (East Siberia, Russia)

This article presents the results of the automatic monitoring of the concentrations of gaseous impurities of sulfur and nitrogen oxides in the ground-level atmosphere of the urban and rural areas in the Southern Baikal region (East Siberia, Russia). The study was conducted from 2020 to 2023 at the urban Irkutsk station and the rural Listvyanka station located at a distance of 70 km from each other. We calculated the main statistical characteristics of the variations in the concentrations of nitrogen oxides and sulfur dioxide in the ground-level atmosphere and determined a nature of variability in their concentrations on various time scales: annual, weekly, and daily. Annual variabilities of gaseous pollutants in the ground-level atmosphere above the Irkutsk city and the Listvyanka settlement were similar and showed the highest values in winter and the lowest in summer. The daily and weekly dynamics of the nitrogen oxide concentrations in the urban area clearly depended on the increase in the road traffic during rush hours (morning and evening). In the rural area, there was no such dependence. In this area, the daily and weekly variability in the concentrations of nitrogen oxides and sulfur dioxide mainly depended on natural meteorological processes. The work systematizes the meteorological parameters at which the largest amount of anthropogenic impurities enters the air basin of Lake Baikal. The maximum values of acid-forming gas concentrations were observed when the air masses were transferred from the northwest direction, which corresponds to the location of sources in the territory of the Irkutsk–Cheremkhovo industrial hub—the largest concentration of anthropogenic objects in the Irkutsk region.

The dominant white color trait of the melon fruit rind is associated with epicuticular wax accumulation.

Microscopic analyses and chemical profiling demonstrate that the white rind phenotype in melon fruit is associated with the accumulation of n-alkanes, fatty alcohols, aldehydes and wax esters. Serving as an indicator of quality, the rind (or external) color of fruit directly affects consumer choice. A fruit's color is influenced by factors such as the levels of pigments and deposited epicuticular waxes. The latter produces a white-grayish coating often referred to as "wax bloom". Previous reports have suggested that some melon (Cucumis melo L.) accessions may produce wax blooms, where a dominant white rind color trait was genetically mapped to a major locus on chromosome 7 and suggested to be inherited as a single gene named Wi. We here provide the first direct evidence of the contribution of epicuticular waxes to the dominant white rind trait in melon fruit. Our light and electron microscopy and gas chromatography-mass spectrometry (GC-MS) comparative analysis of melon accessions with white or green rinds reveals that the rind of melon fruit is rich in epicuticular waxes. These waxes are composed of various biochemical classes, including fatty acids, fatty alcohols, aldehydes, fatty amides, n-alkanes, tocopherols, triterpenoids, and wax esters. We show that the dominant white rind phenotype in melon fruit is associated with increased accumulation of n-alkanes, fatty alcohols, aldehydes and wax esters, which are linked with the deposition of crystal-like wax platelets on their surfaces. Together, this study broadens the understanding of natural variation in an important quality trait of melon fruit and promotes the future identification of the causative gene for the dominant white rind trait.

A natural variation contributes to sugar accumulation in fruit during tomato domestication.

A natural variation contributes to sugar accumulation in fruit during tomato domestication.

Induced and natural variation affect traits independently in hybrid Populus.

The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plant's phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribution to phenotypic effects unclear. The Populus genome is highly polymorphic, and poplars are fairly tolerant of gene dosage variation. Here, using a previously established Populus hybrid F1 population, we assessed and compared the effect of natural allelic variation and induced dosage variation on biomass, phenology and leaf morphology traits. We identified QTLs for many of these traits, but our results indicate limited overlap between the QTLs associated with natural allelic variation and induced dosage variation. Additionally, the integration of data from both allelic and dosage variation identifies a larger set of QTLs that together explain a larger percentage of the phenotypic variance. Finally, our results suggest that the effect of the large indels might mask that of allelic QTLs. Our study helps clarify the relationship between allelic and dosage variation and their effects on quantitative traits.

Concentration Scales and Solvation Thermodynamics: Some Theoretical and Experimental Observations Regarding Spontaneity and the Partition Ratio

The solvation thermodynamics (ST) formalism proposed by A. Ben-Naim is a mathematically rigorous and physically grounded theory for describing properties related to solvation. It considers the solvation process as the transfer of a molecule (“solute”) from a fixed position in the ideal gas phase to a fixed position within the solution. Thus, it removes any contribution to the solvation process that is not related to the interactions between this molecule and its environment in the solution. Because ST is based on statistical thermodynamics, the natural variable is number density, which leads to the amount (or “molar”) concentration scale. However, this choice of concentration scale is not unique in classical thermodynamics and the solvation properties can be different for commonly used concentration scales. We proposed and performed experiments with diethylamine in a water/hexadecane heterogeneous mixture to confront the predictions of the ST, based on the amount (or “molar”) concentration scale, and the Fowler–Guggenheim formalism, based on the mole fraction scale. By means of simple acid–base titration and 1H NMR measurements, it was established that the predictions of differences in the solvation Gibbs energy and the partition ratio (or “partition coefficient”) of diethylamine between water and hexadecane are consistent with the ST formalism. Additionally, with current literature data, we have shown additional experimental support for the ST. However, due to the arbitrariness of the relative amount of solvents in the partition ratio, the choice of a single concentration scale within the classical thermodynamics is still not possible.

Mineralogical Insights into PGM Recovery from Middle Group (1–4) Chromite Tailings

Variations in the recovery of platinum group metals (PGMs) are often attributed to mineralogical and other natural ore-type variations. To increase the recovery of PGMs by the flotation process, a comprehensive understanding of gangue and valuable minerals is essential for optimising the extraction and processing of metals. Recoveries may be improved if the questions of how, where, and why losses occur can be answered with a certain degree of confidence. A requirement is the availability of statistically reliable mineralogical data. The PGMs of MG-1–4 chromite tailings dumps of the western limb of the Bushveld complex (BC) were studied in detail to unravel the PGMs and the nature of the platinum group minerals in the sample. Characterisation of the chromite tailings via deportment analysis revealed that the sample contained a significant amount of 3E PGM + Au (Pt, Pd, Ru, and Au) and was concentrated in the -25 µm fraction. The results of automated mineralogical analysis showed that the sample was composed of the PGE-sulphides group, comprising 63.6 vol%, PGE-sulfarsenides 10.4 vol%, PGE-arsenides 1.3 vol%, PGE-bismuth tellurides 3.3 vol%, PGMs-alloy 4.1 vol%, and Laurite comprising 17.3 vol% of the total PGE population. The sample was composed of 66.5 vol% of liberated PGMs, 0.2 vol% attached to liberated BMS, 27.3 vol% of PGMs attached to or locked within silicate or oxide gangue composite particles, 0.2 vol% of PGMs associated with BMS attached to silicate or oxide gangue particles, and a low proportion (5.8 vol%) of PGMs reported being locked within gangue or oxide particles. The majority of PGM grains observed were reported in the fast-floating category (64.4 vol%), 27.6 vol% in the slow-floating 1 category, 2.2 vol% in the slow-floating 2 category, and 5.8 vol% to the non-floating category. The results of the study revealed that the PGMs of MG 1–4 chromite tailings were liberated; however, the low liberation index (<0.2) suggested that a significant portion of PGMs remained trapped within gangue, hindering their recovery. This highlights the need for effective comminution (crushing and grinding) to achieve better liberation. The sample contained fine particles that were more prone to being lost in the tailings and to lowering recovery due to the slimes coating valuable minerals. The recovery of the PGMs from this complex’s polymetallic bodies of low-grade and complex mineralogy will be insufficient with traditional methods and thus innovation is needed. Innovation like advanced comminution, novel flotation equipment or reagents, selective leaching and bioprocessing can overcome these challenges.

North Atlantic temperature control on deoxygenation in the northern tropical Pacific

Ocean oxygen content is decreasing with global change. A major challenge for modelling future declines in oxygen concentration is our lack of knowledge of the natural variability associated with marine oxygen inventory on interannual and multidecadal timescales. Here, we present 10 annually resolved 200 year-long records of denitrification, a marker of deoxygenation, from a varved sedimentary archive in the North Pacific oxygen minimum zone covering key periods over the last glacial–interglacial cycle. Spectral analyses on these records reveal strong signals at periodicities typical of today’s Atlantic multidecadal oscillation. Modern subsurface circulation reanalyses regressed on the positive Atlantic and Pacific Climatic Oscillation indices further confirm that North Atlantic temperature patterns are the main control on the subsurface zonal circulation and therefore the most likely dominant driver of oxygen variability in the tropical Pacific. With currently increasing temperatures in the Northern Hemisphere high latitudes and North Atlantic, we suggest deoxygenation will intensify in the region.

Drivers of the ECMWF SEAS5 seasonal forecast for the hot and dry European summer of 2022

AbstractThe European summer (June–August) 2022 was characterised by warm and dry anomalies across much of the continent, likely influenced by a northward‐shifted jet stream. These general features were well predicted by European Centre for Medium‐Range Weather Forecasts' system 5 seasonal forecast, initialised on May 1. Such successful predictions for European summers are relatively uncommon, particularly for atmospheric circulation. In this study, a set of hindcast experiments is employed to investigate the role that initialisation of the ocean, atmosphere, and land surface played in the 2022 forecast. We find that the trend from external forcing was the strongest contributor to the forecast near‐surface temperature anomalies, with atmospheric circulation and land‐surface interactions playing a secondary role. On the other hand, atmospheric circulation made a strong contribution to precipitation anomalies. Modelled Euro‐Atlantic circulation anomalies in 2022 were consistent with a La Niña‐forced teleconnection from the tropical Pacific. However, a northward jet trend in the model hindcasts with increasing greenhouse gas concentrations also contributed to the predicted circulation anomalies in 2022. In contrast, the observed linear trend in the jet over the past four decades was a southward shift, though it is unclear whether this trend was driven by external forcings or natural variability. Nevertheless, this case study demonstrates that important features of at least some European summers are predictable at the seasonal time‐scale.

Genome-wide association scan reveals the reinforcing effect of nano-potassium in improving the yield and quality of salt-stressed barley via enhancing the antioxidant defense system.

Salinity is one of themajor environmental factor that can greatly impact the growth, development, and productivity of barley. Our study aims to detect the natural phenotypic variation of morphological and physiological traits under both salinity and potassium nanoparticles (n-K) treatment. In addition tounderstanding the genetic basis of salt tolerance in barley is a critical aspect of plant breeding for stress resilience.Therefore, a foliar application of n-K was applied at the vegetative stage for 138 barley accessions to enhance salt stress resilience. Interestingly, barley accessions showed high significant increment under n-K treatment compared to saline soil. Based on genome-wide association studies (GWAS) analysis, causative alleles /reliable genomic regions were discovered underlying improved salt resilience through the application of potassium nanoparticles. On chromosome 2H, a highly significant QTN marker (A:C) was located at position 36,665,559 bp which is associated with APX, AsA, GSH, GS, WGS, and TKW under n-K treatment. Inside this region, our candidate gene is HORVU.MOREX.r3.2HG0111480 that annotated as NAC domain protein. Allelic variation detected that the accessions carrying C allele showed higher antioxidants (APX, AsA, and GSH) and barley yield traits (GS, WGS, and TKW) than the accessions carrying A allele, suggesting a positive selection of the accessions carrying C allele that could be used to develop barley varieties with improved salt stress resilience.