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Journal articleOlechnowicz A, Blatkiewicz M, Jopek K, et al., 2024,
Deregulated transcriptome as a platform for adrenal Huntington’s disease-related pathology
, International Journal of Molecular Sciences, Vol: 25, ISSN: 1422-0067Huntington’s disease (HD) is a neurodegenerative disorder that affects mainly the central nervous system (CNS) by inducing progressive deterioration in both its structure and function. In recent years, there has been growing interest in the impact of HD on peripheral tissue function. Herein, we used the R6/2 mouse model of HD to investigate the influence of the disease on adrenal gland functioning. A transcriptomic analysis conducted using a well-established quantitative method, an Affymetrix array, revealed changes in gene expression in the R6/2 model compared to genetic background controls. For the first time, we identified disruptions in cholesterol and sterol metabolism, blood coagulation, and xenobiotic metabolism in HD adrenal glands. This study showed that the disrupted expression of these genes may contribute to the underlying mechanisms of Huntington’s disease. Our findings may contribute to developing a better understanding of Huntington’s disease progression and aid in the development of novel diagnostic or therapeutic approaches.
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Journal articleNeyret M, Le Provost G, Boesing AL, et al., 2024,
A slow-fast trait continuum at the whole community level in relation to land-use intensification
, NATURE COMMUNICATIONS, Vol: 15 -
ReportBenton J, Jimenez Zarco J, Banks A, et al., 2024,
Using microbes to remove microplastics from wastewater and sewage sludge
, London, Publisher: Institute for Molecular Science and Engineering, Briefing paper No. 11Microplastics are a widespread form of plastic pollution. There is increasing evidence that they are a threat to human health and the environment. Microplastics in domestic and industrial wastewater become concentrated in sewage sludge during wastewater treatment processes. In 2020, water companies in England produced more than 800,000 tonnes of sewage sludge from urban wastewater. More than 90% of UK sewage sludge is spread on agricultural land as a fertilizer and soil conditioner. This provides a pathway for microplastics to enter the terrestrial environment. There is currently no UK legislation defining safe limits for microplastics in sludge and soils but future regulation is a possibility. There is currently no technology available to remove microplastics from wastewater treatment processes or the resulting sludge. Safe limits for microplastics in treated sewage sludge, soils and water bodies should be identified. This will require a survey of the extent of microplastic pollution throughout the UK, including concentration, identity and characteristics of microplastics in each environmental reservoir, and understanding how microplastics affect different living organisms. Microbes or fungi that break down plastic could be added to existing wastewater treatment process to remove microplastics and prevent their release into the environment. Alternatively, only the active enzymes (rather than the live microorganisms) could be added to the process. Currently, only polyester microplastics (11% of the total microplastic burden) could be treated in this way. Different microorganisms would have to be discovered or developed to tackle other common microplastic polymers such as polypropylene or polyethylene.
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Journal articleDrury JP, Clavel J, Tobias JA, et al., 2024,
Limited ecological opportunity influences the tempo of morphological evolution in birds
, Current Biology, Vol: 34, Pages: 661-669.E4, ISSN: 0960-9822According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.
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Journal articleGuder F, Coatsworth P, Bozkurt O, et al., 2024,
Time-resolved chemical monitoring of whole plant roots with printed electrochemical sensors and machine learning
, Science Advances, Vol: 10, ISSN: 2375-2548Traditional single-point measurements fail to capture dynamic chemical responses of plants, which are complex, nonequilibrium biological systems. We report TETRIS (time-resolved electrochemical technology for plant root environment in situ chemical sensing), a real-time chemical phenotyping system for continuously monitoring chemical signals in the often-neglected plant root environment. TETRIS consisted of low-cost, highly scalable screen-printed electrochemical sensors for monitoring concentrations of salt, pH, and H2O2 in the root environment of whole plants, where multiplexing allowed for parallel sensing operation. TETRIS was used to measure ion uptake in tomato, kale, and rice and detected differences between nutrient and heavy metal ion uptake. Modulation of ion uptake with ion channel blocker LaCl3 was monitored by TETRIS and machine learning used to predict ion uptake. TETRIS has the potential to overcome the urgent “bottleneck” in high-throughput screening in producing high-yielding plant varieties with improved resistance against stress.
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Journal articlePatterson C, Hazime K, Zelenay S, et al., 2024,
Prostaglandin E₂ impacts multiple stages of the natural killer cell antitumor immune response
, European Journal of Immunology, Vol: 54, ISSN: 0014-2980Tumor immune escape is a major factor contributing to cancer progression and unresponsiveness to cancer therapies. Tumors can produce prostaglandin E2 (PGE2), an inflammatory mediator that directly acts on Natural killer (NK) cells to inhibit antitumor immunity. However, precisely how PGE2 influences NK cell tumor-restraining functions remains unclear. Here, we report that following PGE₂ treatment, human NK cells exhibited altered expression of specific activating receptors and a reduced ability to degranulate and kill cancer targets. Transcriptional analysis uncovered that PGE₂ also differentially modulated the expression of chemokine receptors by NK cells, inhibiting CXCR3 but increasing CXCR4. Consistent with this, PGE₂-treated NK cells exhibited decreased migration to CXCL10 but increased ability to migrate toward CXCL12. Using live cell imaging, we showed that in the presence of PGE2, NK cells were slower and less likely to kill cancer target cells following conjugation. Imaging the sequential stages of NK cell killing revealed that PGE₂ impaired NK cell polarization, but not the re-organization of synaptic actin or the release of perforin itself. Together, these findings demonstrate that PGE₂ affects multiple but select NK cell functions. Understanding how cancer cells subvert NK cells is necessary to more effectively harness the cancer-inhibitory function of NK cells in treatments.
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Journal articleD'Amato R, Taxiarchi C, Galardini M, et al., 2024,
Anti-CRISPR <i>Anopheles</i> mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages
, NATURE COMMUNICATIONS, Vol: 15 -
Journal articleAhmadi Y, Umrekar TR, Mutter N, et al., 2024,
DNA origami-enhanced binding of aptamers to Staphylococcus aureus cells
, Biosensors and Bioelectronics: X, Vol: 16The combination of DNA origami nanostructures and aptamers provides a powerful technology for diagnostic assays. Here, we functionalized a DNA origami nanostructure with a Protein-A binding aptamer to target Staphylococcus aureus bacterial cells. Using an enzyme-linked oligonucleotide assay (ELONA), we semi-quantitatively analyzed and compared the interaction of the aptamer and aptamer-modified DNA origamis with Staphylococcus aureus bacterial isolates. The results showed that aptamer-functionalized DNA nanostructures bind with five times higher affinity (KD: 34 ± 5 nM) compared to the aptamer alone (KD: 160 ± 9 nM). Visualising the interaction of bacterial cells and nanostructures with electron cryotomography further confirmed the aptamer-mediated specific interaction of DNA nanostructures with bacterial cells.
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Journal articleKaramanos TK, Matthews S, 2024,
Biomolecular NMR in the AI-assisted structural biology era: Old tricks and new opportunities
, BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, Vol: 1872, ISSN: 1570-9639 -
Journal articleMutemi DD, Tuju J, Ogwang R, et al., 2024,
Antibody-dependent respiratory burst against Plasmodium falciparum Merozoites in individuals living in an area with declining malaria transmission
, Vaccines, Vol: 12, ISSN: 2076-393XMalaria transmission intensity affects the development of naturally acquired immunity to malaria. An absolute correlate measure of protection against malaria is lacking. However, antibody-mediated functions against Plasmodium falciparum correlate with protection against malaria. In children, antibody-mediated functions against P. falciparum decline with reduced exposure. It is unclear whether adults maintain antibody-mediated functions as malaria transmission declines. This study assessed antibody-dependent respiratory burst (ADRB) in individuals from an area with declining malaria transmission. In an age-matched analysis, we compare ADRB activity during high versus low malaria transmission periods. Age significantly predicted higher ADRB activity in the high (p < 0.001) and low (p < 0.001) malaria transmission periods. ADRB activity was higher during the high compared to the low malaria transmission period in older children and adults. Only older adults during the high malaria transmission period had their median ADRB activity above the ADRB cut-off. Ongoing P. falciparum infection influenced ADRB activity during the low (p = 0.01) but not the high (p = 0.29) malaria transmission period. These findings propose that naturally acquired immunity to P. falciparum is affected in children and adults as malaria transmission declines, implying that vaccines will be necessary to induce and maintain protection against malaria.
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Journal articleArraiano-Castilho R, Bidartondo MI, Niskanen T, et al., 2024,
Climatic shifts threaten alpine mycorrhizal communities above the treeline
, FUNGAL ECOLOGY, Vol: 67, ISSN: 1754-5048 -
Journal articleKeeping T, Harrison SP, Prentice IC, 2024,
Modelling the daily probability of wildfire occurrence in the contiguous United States
, Environmental Research Letters, Vol: 19, ISSN: 1748-9326The development of a high-quality wildfire occurrence model is an essential component in mapping present wildfire risk, and in projecting future wildfire dynamics with climate and land-use change. Here, we develop a new model for predicting the daily probability of wildfire occurrence at 0.1° (∼10 km) spatial resolution by adapting a generalised linear modelling (GLM) approach to include improvements to the variable selection procedure, identification of the range over which specific predictors are influential, and the minimisation of compression, applied in an ensemble of model runs. We develop and test the model using data from the contiguous United States. The ensemble performed well in predicting the mean geospatial patterns of fire occurrence, the interannual variability in the number of fires, and the regional variation in the seasonal cycle of wildfire. Model runs gave an area under the receiver operating characteristic curve (AUC) of 0.85–0.88, indicating good predictive power. The ensemble of runs provides insight into the key predictors for wildfire occurrence in the contiguous United States. The methodology, though developed for the United States, is globally implementable.
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Journal articleMolnar Z, Aumeeruddy-Thomas Y, Babai D, et al., 2024,
Towards richer knowledge partnerships between ecology and ethnoecology
, TRENDS IN ECOLOGY & EVOLUTION, Vol: 39, Pages: 109-115, ISSN: 0169-5347 -
Journal articleCurrie D, Wong N, Zane I, et al., 2024,
A Potential Prognostic Gene Signature Associated with p53-Dependent NTRK1 Activation and Increased Survival of Neuroblastoma Patients
, CANCERS, Vol: 16 -
Journal articleGranville NR, Barclay MVL, Boyle MJW, et al., 2024,
Resilience of tropical invertebrate community assembly processes to a gradient of land use intensity
, OIKOS, Vol: 2024, ISSN: 0030-1299Understanding how community assembly processes drive biodiversity patterns is a central goal of community ecology. While it is generally accepted that ecological communities are assembled by both stochastic and deterministic processes, quantifying their relative importance remains challenging. Few studies have investigated how the relative importance of stochastic and deterministic community assembly processes vary among taxa and along gradients of habitat degradation. Using data on 1645 arthropod species across seven taxonomic groups in Malaysian Borneo, we quantified the importance of ecological stochasticity and of a suite of community assembly processes across a gradient of logging intensity. The relationship between logging and community assembly varied depending on the specific combination of taxa and stochasticity metric used, but, in general, the processes that govern invertebrate community assembly were remarkably robust to changes in land use intensity.
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Journal articleCruz-Silva E, Harrion SP, Prentice IC, et al., 2024,
Holocene vegetation dynamics of the Eastern Mediterranean region: old controversies addressed by a new analysis
, Journal of Biogeography, Vol: 51, Pages: 294-310, ISSN: 0305-0270Aim:We reconstruct vegetation changes since 12 ky in the Eastern Mediterranean to examine four features of the regional vegetation history that are controversial: the extent of non-analogue vegetation assemblages in the transition from the Late Glacial to the early Holocene, the synchroneity of postglacial forest expansion, the geographical extent of temperate deciduous forest during the mid-Holocene and the timing and trigger for the re-establishment of drought-tolerant vegetation during the late Holocene.Location:The Eastern Mediterranean–Black Sea Caspian Corridor.Taxon:Vascular plants.Methods:We reconstruct vegetation changes for 122 fossil pollen records using a method that accounts for within-biome variability in pollen taxon abundance to determine the biome with which a sample has greatest affinity. Per-biome affinity threshold values were used to identify samples that do not belong to any modern biome. We apply time series analysis and mapping to examine space and time changes.Results:Sites with non-analogue vegetation were most common between 11.5 and 9.5 ky and mostly in the Carpathians. The transition from open vegetation to forest occurred at 10.64 ± 0.65 ky across the whole region. Temperate deciduous forest was not more extensive at 6 ky; maximum expansion occurred between 5.5 and 5 ky. Expansion of forest occurred between c. 4 and 2.8 k, followed by an abrupt decrease and a subsequent recovery. This pattern is not consistent with a systematic decline of forest towards more drought-tolerant vegetation in the late Holocene but is consistent with centennial-scale speleothem patterns linked to variations in moisture availability.Main Conclusions:We show the occurrence of non-analogue vegetation types peaked during early Holocene, forest expansion was synchronous across the region and there was an expansion of moisture-demanding temperate trees around 5.5 to 5 ky. There is no signal of a continuous late Holocene aridificat
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Journal articleHatfield JH, Banks-Leite C, Barlow J, et al., 2024,
Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests
, FUNCTIONAL ECOLOGY, Vol: 38, Pages: 315-326, ISSN: 0269-8463 -
Journal articleBasu S, Shukron O, Hall D, et al., 2024,
Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD ( vol 30 , pg 1628 , 2023)
, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 31, Pages: 390-390, ISSN: 1545-9993 -
Journal articleCretois B, Bick IA, Balantic C, et al., 2024,
Snowmobile noise alters bird vocalization patterns during winter and pre-breeding season
, JOURNAL OF APPLIED ECOLOGY, Vol: 61, Pages: 340-350, ISSN: 0021-8901 -
Journal articleLiu Y, Olsson A, Larva T, et al., 2024,
Genomic variation in montane bumblebees in Scandinavia: high levels of intraspecific diversity despite population vulnerability.
, Molecular Ecology, Vol: 33, ISSN: 0962-1083Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.
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Journal articleLeung PB, Matanza XM, Roche B, et al., 2024,
<i>Shigella</i><i> sonnei</i> utilises colicins during inter- bacterial competition
, MICROBIOLOGY-SGM, Vol: 170, ISSN: 1350-0872 -
Journal articleSchuster M, Eisele S, Armas-Egas L, et al., 2024,
Enhanced late blight resistance by engineering an EpiC2B-insensitive immune protease
, Plant Biotechnology Journal, Vol: 22, Pages: 284-286, ISSN: 1467-7644Papain-like immune proteases (PLCPs) are promising engineering targets for crop protection, given their significant roles in plant immunity for key crops such as tomato, maize and citrus (Misas-Villamil et al., 2016). The wide range of pathogen-secreted PLCP inhibitors highlights the importance of these proteases in defending against various pathogens. Depletion of the apoplastic immune PLCP Phytophthora-inhibited protease 1 (Pip1) from tomato, for instance, causes hyper-susceptibility to bacterial, fungal and oomycete tomato pathogens (Ilyas et al., 2015). Immunity by Pip1 in wild-type tomato is, however, suboptimal since Pip1 is suppressed during infection by diverse pathogen-secreted inhibitors, such as the cystatin-like EpiC2B from the oomycete late blight pathogen Phytophthora infestans (Tian et al., 2007). Here, we tested whether we could increase Pip1-based immunity against late blight by engineering Pip1 into an EpiC2B-insensitive protease. To guide Pip1 mutagenesis, we generated a structural model of the EpiC2B-Pip1 complex using AlphaFold-Multimer (Evans et al., 2022). This structural model represents a classic interaction between the tripartite wedge of cystatin (EpiC2B) in the substrate binding groove of papain (Pip1). This model indicated that engineering Pip1 to prevent inhibition without affecting Pip1 substrate specificity is possible because the interaction surface of Pip1 with EpiC2B is larger than the substrate binding groove (Figure 1a).
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Journal articleMajumdar A, Moulick D, Srivastava S, 2024,
Editorial: ‘Save Soil' by managing soil nutrient losses, agronomic practices and crop-microbial interaction: World Soil Day 2022
, Frontiers in Sustainable Food Systems, Vol: 8 -
Journal articleCantwell-Jones A, Tylianakis J, Larson K, et al., 2024,
Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change
, Ecology Letters, Vol: 27, ISSN: 1461-023XDetermining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.
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ReportWaring BG, 2024,
The potential for enhanced soil carbon sequestration to mitigate climate change
This briefing note assesses the potential for soil carbon sequestration to mitigate climate change, summarising the basic science and providing an overview of best practices for measuring and modifying soil carbon stocks. We also set out recommendations for policy makers, examining UK land use policies as a case study.
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Journal articleLi S, Waring B, Powers J, et al., 2024,
Tropical dry forest response to nutrient fertilization: a model validation and sensitivity analysis
, BIOGEOSCIENCES, Vol: 21, Pages: 455-471, ISSN: 1726-4170 -
Journal articleWan Y, Myall AC, Boonyasiri A, et al., 2024,
Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes
, Journal of Infectious Diseases, ISSN: 0022-1899BackgroundCarbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)–encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.MethodsWe performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE–positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.ResultsGenomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.ConclusionsCombined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.
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Journal articleMoulick D, Mukherjee A, Das A, et al., 2024,
Selenium - An environmentally friendly micronutrient in agroecosystem in the modern era: An overview of 50-year findings.
, Ecotoxicol Environ Saf, Vol: 270Agricultural productivity is constantly being forced to maintain yield stability to feed the enormously growing world population. However, shrinking arable and nutrient-deprived soil and abiotic and biotic stressor (s) in different magnitudes put additional challenges to achieving global food security. Though well-defined, the concept of macro, micronutrients, and beneficial elements is from a plant nutritional perspective. Among various micronutrients, selenium (Se) is essential in small amounts for the life cycle of organisms, including crops. Selenium has the potential to improve soil health, leading to the improvement of productivity and crop quality. However, Se possesses an immense encouraging phenomenon when supplied within the threshold limit, also having wide variations. The supplementation of Se has exhibited promising outcomes in lessening biotic and abiotic stress in various crops. Besides, bulk form, nano-Se, and biogenic-Se also revealed some merits and limitations. Literature suggests that the possibilities of biogenic-Se in stress alleviation and fortifying foods are encouraging. In this article, apart from adopting a combination of a conventional extensive review of the literature and bibliometric analysis, the authors have assessed the journey of Se in the "soil to spoon" perspective in a diverse agroecosystem to highlight the research gap area. There is no doubt that the time has come to seriously consider the tag of beneficial elements associated with Se, especially in the drastic global climate change era.
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Journal articleWorboys JD, Davis DM, 2024,
Do inhibitory receptors need to be proximal to stimulatory receptors to function?
, GENES AND IMMUNITY, ISSN: 1466-4879 -
Journal articleSavolainen V, Bailey NW, Diamond L, et al., 2024,
A broader cultural view is necessary to study the evolution of sexual orientation
, Nature Ecology and Evolution, Vol: 8, Pages: 181-183, ISSN: 2397-334XThe causation of sexual orientation is likely to be complex and influenced by multiple factors1. We advocate incorporating a broader cultural view into evolutionary andgenetic studies to account for differences in how sexual orientation is experienced, expressed, and understood in both human and non-human animals.
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