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6,234 results for “phenotypes”
Maximization of fitness by phenological and phenotypic plasticity in range expanding rabbitfish (Siganidae)
<p>Global warming is modifying the phenology, life-history traits and biogeography of species around the world. Evidence of these effects have increased over recent decades; however, we still have a poor understanding of the possible outcomes of their interplay across global climatic gradients, hindering our ability to accurately predict the consequences of climate change in populations and ecosystems. We examined the effect that changes in biogeography can have on the life-history traits of two of the most successful range-extending fish species in the world: the tropical rabbitfishes Siganus fuscescens and Siganus rivulatus. Both species have established abundant populations at higher latitudes (poleward) in the northern and southern hemispheres and have been identified as important ecological engineers with the potential to alter the community structure of seaweed forests (Laminariales and Fucales) in temperate regions. Life-history trait information from across their global distribution was compiled from the published literature and meta-analyses were conducted to assess changes in (i) the onset and duration of reproductive periods, (ii) fecundity, (iii) size at maturity, (iv) growth rates, (v) maximum body sizes and (vi) longevity in populations at the leading edge of range expansion in relation to sea surface temperature and primary productivity (i.e., a common proxy for nutritional resource levels). Populations at highest latitudes had shortened their reproductive periods and reduced growth rates, taking longer to reach sexual maturity and maximum sizes, but compensated this with higher fecundity per length class and longer lifespans than populations in warmer environments. Low primary productivity and temperature in the Mediterranean Sea resulted in lower growth rates and body sizes for S. rivulatus, but also lower length at maturity, leading to increased life-time reproductive output. The results suggest that plasticity in the phenology and life-history traits of range-expanding species would be important to enhance their fitness in high latitude environments, facilitating their persistence and possible further poleward expansions. Quantifying the magnitude and direction of these responses can improve our understanding and ability to forecast species redistributions and its repercussions in the functioning of temperate ecosystems. </p>
Phenotypic correlates of pelvic spine coloration in the Threespine Stickleback (Gasterosteus aculeatus): Implications for function and evolution
<p>Animal color patches may be static or plastic in expression and concealable or continuously visible, yet these aspects of coloration, and their consequences, have been little studied. We address them here using the threespine stickleback (<em>Gasterosteus aculeatus</em>). Despite a rich history of study of stickleback nuptial color pattern evolution, disagreement persists regarding selection pressures and function. However, little research has addressed the role of pelvic spine coloration, a potentially important, and substantially concealable, color pattern element. We investigated (i) whether male pelvic spine (along with throat and body) coloration is relatively static or plastic across the reproductive cycle, (ii) when pelvic spines are raised versus concealed across behavioral contexts, and (iii) associations between color patches and behavior in males. We found no significant variation in spine color across reproductive stages whereas body color was more plastic and intensely red during courtship and egg/fry care. Conspicuousness of pelvic spine coloration instead varied behaviorally, through increased erection frequency during social interactions and in response to a model predator. Spine erection frequency was positively associated with behaviors that enhance spine color visibility, i.e. flees and leads to nest. These findings suggest that stickleback use pelvic spines to display an intensely red color patch facultatively, either as a complement to similar body coloration or possibly as a substitute. In addition, elevated spine raising in the presence of a model predator, together with the presence of red spine coloration in females, raises the possibility that red spine coloration may also have an anti-predator function.</p>
Provenance rather than nitrogen addition dominate the phenotypes and plasticity of Ambrosia artemisiifolia in China
<p><span>Phenotypic plasticity, which differs between species, populations, individuals, even traits, is considered as one of the mechanisms of plant invasion. We conducted a common garden experiment with six provenances (HRB, CC, HG, ML, MZ, LB) of <em>Ambrosia artemisiifolia</em> and three nitrogen addition treatments to test their performance response. In order to explore the adaptation strategies of <em>A. artemisiifolia </em>towards heterogeneous habitats, phenotypic plasticity indexes were calculated to analyze among different provenances and traits. All traits were significantly influenced (<em>P</em><0.05) by provenance, except for number of inflorescences, inflorescences length and intercellular CO<sub>2</sub> concentration. Nitrogen addition notably affected on seed length, root biomass ratio, root-shoot ratio and four physiological traits (Pn, Tr, Gs, Ci). Among six provenances, the phenotypic plasticity index differed significantly (<em>P</em><0.05), but there were no significant differences of plasticity among nitrogen treatments. And biomass phenotypic plasticity was relatively higher both in response to prevenance and to nitrogen. We also found that only the plasticity of 100-seed weight was closely related to latitude, climate and genetic factors. In summary, provenances had a greater impact on the phenotype and plasticity of <em>A. artemisiifolia</em> than nitrogen addition, indicating the potential for further evolution of plasticity. Differences in plasticity among provenances and traits are important in predicting the invasion trend of <em>A. artemisiifolia</em> in the future.</span></p>
Data from: Hierarchical variation in phenotypic flexibility across timescales and associated survival selection shape the dynamics of partial seasonal migration
<p>Population responses to environmental variation ultimately depend on within-individual and among-individual variation in labile phenotypic traits that affect fitness, and resulting episodes of selection. Yet, complex patterns of individual phenotypic variation arising within and between time periods, and associated variation in selection, have not been fully conceptualised or quantified. We highlight how structured patterns of phenotypic variation in dichotomous threshold traits can theoretically arise and experience varying forms of selection, shaping overall phenotypic dynamics. We then fit novel multistate models to ten years of band-resighting data from European shags to quantify phenotypic variation and selection in a key threshold trait underlying spatio-seasonal population dynamics: seasonal migration versus residence. First, we demonstrate substantial among-individual variation alongside substantial between-year individual repeatability in within-year phenotypic variation ('flexibility'), with weak sexual dimorphism. Second, we demonstrate that between-year individual variation in within-year phenotypes ('supraflexibility') is structured and directional, consistent with the threshold trait model. Third, we demonstrate strong survival selection on within-year phenotypes, and hence on flexibility, that varies across years and sexes, including episodes of disruptive selection representing costs of flexibility. By quantitatively combining these results, we show how supraflexibility and survival selection on migratory flexibility jointly shape population-wide phenotypic dynamics of seasonal movement.</p>
A high-throughput assay for quantifying phenotypic traits of microalgae
<p>High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell size, granularity, chlorophyll a, neutral lipid content, silicification, reactive oxygen species accumulation, and photophysiology parameters: ETRmax, Ik, and alpha) into one workflow. We demonstrate the utility of the QPA on Thalassiosira spp., a cosmopolitan marine diatom, phenotyping six strains in a standard nutrient rich environment (f/2 media) using the full 10-trait assay. The multivariate phenotypes of strains can be simplified into two dimensions using principal component analysis, generating a trait-scape. We determine that traits show a consistent pattern when grown in small volume compared to more typical large volumes. The QPA can thus be used for quantifying traits across different growth environments without requiring exhaustive large-scale culturing experiments, which facilitates experiments on trait plasticity. We confirm that this assay can be used to phenotype newly isolated diatom strains within 4 weeks of isolation. The QPA described here is highly amenable to customisation for other traits or unicellular taxa and provides a framework for designing high-throughput experiments. This method will have applications in experimental evolution, modelling, and for commercial applications where screening of phytoplankton traits is of high importance.</p>
Mandrill mothers associate with infants who look like their own offspring using phenotype matching
<p>Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide a first example of discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally-related juvenile and adult females indicating adaptive opportunities for paternal kin recognition. Here, we hypothesize that mothers use offspring's facial resemblance with other infants to guide offspring's social opportunities towards similarly-looking ones. Using deep learning for face recognition in 80 wild mandrill infants, we first show that infants born to the same father or conceived during the tenure of the same alpha male resemble each other the most, independently of their age, sex or maternal origin, extending previous results to the youngest age class. Using long-term behavioral observations on association patterns and controlling for matrilineal origin, maternal relatedness and infant age and sex, we then demonstrate that, as hypothesized, mothers are spatially closer to infants that resemble their own offspring more, thereby facilitating associations among similar-looking infants. Using theoretical modeling, we describe a plausible evolutionary process whereby mothers gain fitness benefits by promoting nepotism among paternally related infants. This mechanism, that we call "second order kin selection", may extend beyond mother-infant interactions and has the potential to explain cooperative behaviors among non-kin in social species, including humans.</p>
Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird
<p>Aim: Along with environmental gradients, some species show significant differences in morphological, ecological-related traits. Those differences are commonly related to past events of allopatry but, alternatively, could be caused by natural selection in the presence of gene flow. We aimed to explore the prevalence of the divergence-with-gene-flow model across the Chaco-Andes dry forest belt, testing competing models of evolution in a Neotropical bird.</p> <p>Location: Central Andes Mountain range and Chaco region of Argentina and Bolivia. </p> <p>Taxon: Phytotoma rutila (Aves, Cotingidae).</p> <p>Methods: We studied ddRADseq loci (4,893 SNPs) of 21 tissue samples and body size variation of 146 specimens. We evaluated population genetic structure and tested the effects of altitude and distance on genomic divergence. To evaluate allopatry and divergence-with-gene-flow, we compared the divergence on phenotypic traits (bill, tarsus, and wing measurements) versus neutral genomic variation, conducted coalescent analyses to estimate gene flow and divergence time among populations, and calculated relative (FST) versus absolute (DXY) genomic divergence.</p> <p>Results: a) there is a genomic and phenotypic differentiation in P. rutila matched the highland-lowland axis, where the altitude variation explains genomic variation; b) A larger phenotypic than neutral genomic variation was found. c) there is an asymmetric gene flow between populations; d) a pattern of relative and absolute genomic differentiation compatible with divergence-with-gene-flow.</p> <p>Main conclusions: The mechanism behind the morphological and genomic diversification along the Chaco-Andes dry forest belt in P. rutila is divergence‐with‐gene‐flow. Far more complex than we traditionally thought, diversification in South America implicates gene flow between populations and also natural selection along with the environmental gradients, as well as vicariance, contrasting with the idea of tropical speciation primarily based on allopatric models.</p> <p> </p>
Environmental change and the rate of phenotypic plasticity
<p class="TREEsubmission"><span>With rapid and less predictable environmental change emerging as the 'new norm', understanding how individuals tolerate environmental stress via plastic, often reversible changes to the phenotype (i.e. reversible phenotypic plasticity, RPP) remains a key issue in ecology. Here, we examine the potential for better understanding how organisms overcome environmental challenges within their own lifetimes by scrutinizing a somewhat overlooked aspect of RPP, namely the rate at which it can occur. Whilst recent advances in the field provide indication of the aspects of environmental change where RPP rates may be of particular ecological relevance, we observe that current theoretical models do not consider the evolutionary potential of the rate of RPP. Although, recent theory underscores the importance of environmental predictability in determining the slope of the evolved reaction norm for a given trait (i.e. how much plasticity can occur), a hitherto neglected possibility is that the rate of plasticity might be a more dynamic component of this relationship than previously assumed. If the rate of plasticity itself can evolve, as empirical evidence foreshadows rates of plasticity may have the potential to alter the level predictability in the environment as perceived by the organism and thus influence the slope of the evolved reaction norm. However, optimality in the rate of phenotypic plasticity, its evolutionary dynamics in different environments and influence of constraints imposed by associated costs remain unexplored and may represent fruitful avenues of exploration in future theoretical and empirical treatments of the topic. We conclude by reviewing published studies of RPP rates, providing suggestions for improving the measurement of RPP rates, both in terms of experimental design and in the statistical quantification of this component of plasticity.</span></p> <p> </p>
Temocillin susceptibility in Enterobacterales with an ESBL/AmpC phenotype
<p>Carbapenems are considered the drugs of choice for first-line treatment of severe infections caused by carbapenem-susceptible<b>, </b>extended-spectrum β-lactamases (ESBL)-producing Enterobacterales, while piperacillin-tazobactam has been recommended as an alternative for treatment of non-severe infections. Temocillin is <em>stable to ESBL and AmpC enzymes</em> and may thus represent another treatment option<em>. </em><span>This study assessed the <i>in vitro</i> activity of piperacillin-tazobactam and temocillin against third-generation cephalosporin (3GC)-resistant <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i>, </span><span>as compared to </span><span>3GC-susceptible isolates of either species</span><span>.</span></p> <p>One hundred and nine isolates from hospitalised patients with bloodstream and urinary tract infections were tested. All isolates were collected during the<span> resistance surveillance study of the Paul-Ehrlich-Society for Chemotherapy in</span> 2016/17. Minimum inhibitory concentrations (MICs) were determined by broth microdilution according to the standard ISO 20776-1 and interpreted using EUCAST clinical breakpoints (version 11.0).</p> <p>Seventy-nine isolates (<i>E. coli</i>, n = 58; <i>K. pneumoniae</i>, n = 21) were 3GC-resistant and 30 (<i>E. coli</i>, n = 15; <i>K. pneumoniae</i>, n = 15) were 3GC-susceptible. Susceptibility to piperacillin-tazobactam was detected in 93.7 % of 3GC-susceptible isolates (for both <i>E. coli</i> and <i>K. pneumoniae</i>) and in 79.3 % and 57.1 % of the 3GC-resistant <i>E. coli</i> and <i>K. pneumoniae</i>, respectively. In contrast, 3GC-susceptible isolates were 100% susceptible to temocillin as were 94.8% and 90.5% of the 3GC-resistant <i>E. coli</i> and <i>K. pneumoniae</i>, respectively.</p> <p>In conclusion, temocillin demonstrated potent <i>in vitro</i> activity against carbapenem-susceptible, 3GC-resistant <i>E. coli</i> and <i>K. pneumoniae</i> from bloodstream and urinary tract infection samples, with susceptibility rates exceeding those of piperacillin-tazobactam.</p>
Single-cell phenotypic characteristics of tolerance under recurring antibiotic exposure in Escherichia coli
<p>Non-heritable drug resistance, such as tolerance and persistence towards antibiotics, is little characterized compared to genetic resistance. Tolerance and persistence allow cells to survive application of antibiotics that are bactericidal to non-tolerant cells. Non-heritable drug resistance challenges antibiotic treatment, particularly of recurrent infections, and have implications towards heritable resistance evolution. Tolerant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we explore characteristic of tolerant and susceptible <em>E. coli</em> single bacteria cells to different levels of recurrent antibiotic exposure and quantify their occurrence. In using a high throughput single-cell microfluidic device, we find that tolerant cells reduce their growth rate by about 50%, but contrary to previous findings do not go into growth arrest or near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as previously described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and selection did not primarily act on fast growing cells, as expected for a β-lactam antibiotic. Control experiments on population cultures confirmed and challenged scaling of single cell findings to population level processes. Our findings suggest a prevalent type of tolerance that differs from previously described tolerance and persister characteristics. Our described characteristics and its high frequency of occurrence supports acclaims of an underappreciated role of tolerant cells towards resistance evolution.</p>
Natural distribution and phenotypic traits of Prosopis flexuosa var. depressa in Argentina
<p>Table S1: Registered information of collection site, and environment (soil and climate).</p> <p>Table S2: Spinescence of adult plant in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S3: Soil seed bank persistence of Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S4: Seeds sown and seedlings established to the phenotypic traits evaluation in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S5: Seedling traits of Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S6: Pearson's correlation of seedling traits in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p>
High within-clutch repeatability of eggshell phenotype in Barn Swallows (Hirundo rustica erythrogaster) despite less maculated last-laid eggs
<p>Ecological and life history variation and both interspecific and intraspecific brood parasitism contribute to diversity in egg phenotype within the same species. In this study, Barn Swallows (<em>Hirundo rustica erythrogaster</em>) laid eggs with high intraclutch repeatability in egg size, shape, and maculation. Despite this high intraclutch repeatability, last-laid eggs had consistently less of the eggshell covered in spots and fewer spots than earlier-laid eggs in the clutch. We examined sources of interclutch and intraclutch variation using both direct measurements and custom-software (SpotEgg, NaturePatternMatch) that provide detailed information on egg characteristics, especially maculation measures. In addition to our main findings, maculation on different sides of the egg was highly repeatable; however, only shape, proportion of the eggshell maculated, and average spot size were repeatable between first and replacement clutches. Low intraclutch variation in maculation could allow females to recognize their clutch and this may be adaptive for colonial nesting species, such as the Barn Swallow. Characterizing intraspecific variation in egg size, shape, and maculation is the first step in understanding whether intraclutch variation is low enough - and interclutch variation high enough – such that eggs could serve as identity signals.</p>
Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga
<p>Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in <em>Dunaliella salina</em>, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - albeit significant - effect of strain × environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in <em>trans</em> that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.</p>
Data for PNASnexus article Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype
<p>Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from <em>Aldh3a1</em>-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.</p>
Multimodal single cell analysis of the paediatric lower airway reveals novel immune cell phenotypes in early life health and disease
<p>RDS files of SingleCellExperiment objects containing raw single cell RNA-seq count data required to replicate the analyses presented at: <a href="https://oshlacklab.com/paed-cf-cite-seq/">https://oshlacklab.com/paed-cf-cite-seq/</a> and described in the pre-print titled: <em>"</em>Multimodal single cell analysis of the paediatric lower airway reveals novel immune cell phenotypes in early life health and disease<em>"</em>.<br> Instructions for how to incorporate the raw data into the analysis can be found at: <a href="https://oshlacklab.com/paed-cf-cite-seq/gettingStarted.html">https://oshlacklab.com/paed-cf-cite-seq/gettingStarted.html</a> and the complete analysis code and additional data files can be cloned/downloaded from: <a href="https://github.com/Oshlack/paed-cf-cite-seq">https://github.com/Oshlack/paed-cf-cite-seq</a>.</p>
Phenotypic plasticity and the leaf economics spectrum: plasticity is positively associated with specific leaf area
<p>Phenotypic plasticity is a key mechanism by which plants respond to changing or heterogeneous conditions. Efforts to predict phenotypic plasticity across plant species have mainly focused on environmental variability or abiotic conditions, i.e., site characteristics. However, the considerable variation in phenotypic plasticity within sites calls for alternative approaches. Different functional groups are thought to differ in their plasticity levels. Further, traits such as leaf specific area (SLA), leaf area (LA) and maximum photosynthetic rate (Amax) reflect central aspects of plant strategies. Lower values of SLA, LA and Amax are indicative of a resource-conservative strategy, which is thought to be associated with lower phenotypic plasticity. We used meta-analytical data to test whether plant functional group (herbs, woody deciduous and woody evergreens) and SLA, LA and Amax are associated with phenotypic plasticity in four trait types: biomass allocation, plant size, leaf morphology and physiology. We obtained data from 168 plant species and accounted for phylogenetic relationships in all analyses. We found a positive relationship between SLA and phenotypic plasticity in biomass allocation, leaf morphology and physiology, with differences across functional groups. In contrast, there was no evidence of greater plasticity in plant size in species with higher SLA; rather the opposite was true for woody evergreens. Amax and LA showed similar, but less consistent associations with phenotypic plasticity. Our results show the potential of building predictive frameworks for phenotypic plasticity based on easily measured plant functional characteristics. Results also provide insights into plant strategies and suggest the existence of potential compromises: resource-conservative, low-SLA species tend to be more stress-tolerant but may be less able to cope with variable conditions due to their generally lower phenotypic plasticity. Further studies are needed to explore the mechanisms and the potential implications of this association.</p>
Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant
<p>A road-map of the genetic and phenotypic diversities in both crops and their wild-related species can help identifying valuable genetic resources for further crop breeding. The clary sage (<em>Salvia sclarea L.</em>), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sage remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild <em>S. sclarea</em> populations from Croatia, sampled along an altitudinal gradient, and of populations of three <em>S. sclarea</em> cultivars. We showed low level of genetic diversity for the two <em>S. sclarea</em> traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.</p>
Data from: A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes
<p><strong>Background: </strong>The large inter-individual variability in immune-cell cell composition and function determines immune responses in general and susceptibility to immune-mediated diseases in particular. While much has been learned about the genetic variants relevant for type 1 diabetes (T1D), the pathophysiological mechanisms through which these variations exert their effects remain unknown.</p> <p><strong>Methods:</strong> Blood samples were collected from 243 patients with T1D of Dutch descent. We applied genetic association analysis on > 200 immune cell traits and >100 cytokine production profiles in response to stimuli measured to identify genetic determinants of immune function, and compared the results obtained in T1D to healthy controls.</p> <p><strong>Results:</strong> Genetic variants that determine susceptibility to T1D significantly affect T cell composition. Specifically, the CCR5+ regulatory T cells associate with T1D through the CCR region, suggesting a shared genetic regulation. Genome-wide quantitative trait loci (QTL) mapping analysis of immune traits revealed 15 genetic loci that influence immune responses in T1D, including 12 that have never been reported in healthy population studies, implying a disease-specific genetic regulation.</p> <p><strong>Conclusion:</strong> This study provides new insights into the genetic factors that affect immunological responses in T1D.</p>
Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation
Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade-Saxifragales-with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (~15 mya), followed by increases in niche and phenotypic evolutionary rates by ~5 mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.
DYRK1a inhibitor mediated rescue of Drosophila models of Alzheimer's disease-Down Syndrome phenotypes
<p>Alzheimer's disease (AD) is the most common neurodegenerative disease which is becoming increasingly prevalent due to ageing populations resulting in huge social, economic, and health costs to the community. Despite the pathological processing of genes such as Amyloid Precursor Protein (APP) into Amyloid-b and Microtubule Associated Protein Tau (MAPT) gene, into hyperphosphorylated Tau tangles being known for decades, there remains no treatments to halt disease progression. One population with increased risk of AD are people with Down syndrome (DS), who have a 90% lifetime incidence of AD, due to trisomy of human chromosome 21 (HSA21) resulting in three copies of APP and other AD-associated genes, such as DYRK1A (Dual specificity tyrosine-phosphorylation-regulated kinase 1A) overexpression. This suggests that blocking DYRK1A might have therapeutic potential. However, it is still not clear to what extent DYRK1A overexpression by itself leads to AD-like phenotypes and how these compare to Tau and Amyloid-b mediated pathology. Likewise, it is still not known how effective a DYRK1A antagonist may be at preventing or improving any Tau, Amyloid-b and DYRK1a mediated phenotype. To address these outstanding questions, we characterised Drosophila models with targeted overexpression of human Tau, human Amyloid-b or the fly orthologue of DYRK1A, called minibrain (mnb). We found targeted overexpression of these AD-associated genes caused degeneration of photoreceptor neurons, shortened lifespan, as well as causing loss of locomotor performance, sleep, and memory. Treatment with the experimental DYRK1A inhibitor PST-001 decreased pathological phosphorylation of human Tau (at serine (S) 262). PST-001 reduced degeneration caused by human Tau, Amyloid-b or mnb lengthening lifespan as well as improving locomotion, sleep and memory loss caused by expression of these AD and DS genes. This demonstrated PST-001 effectiveness as a potential new therapeutic targeting AD and DS pathology.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.