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7,327 results for “Pathway”
Data from: Curcumin improves glycolipid metabolism through regulating peroxisome proliferator activated receptor γ signalling pathway in high-fat diet-induced obese mice and 3T3-L1 adipocytes
Curcumin, an active component derived from the Curcuma longa L. which is a traditional Chinese medicine that is widely used for treating metabolic diseases through regulating different molecular pathway. Here, in this study, we aimed to comprehensively investigate the effects of curcumin on glycolipid metabolism in vivo and in vitro and then determine the underlying mechanism. Male C57BL/6J obese mice and 3T3-L1 adipocytes were used in vivo and in vitro study, respectively. Our results demonstrated that treatment with curcumin for 8 weeks decreased body weight, fat mass and serum lipid profiles. Meanwhile, it lowered fasting blood glucose and increased the insulin sensitivity in high-fat diet induced obese mice. In addition, curcumin stimulated lipolysis and improve glycolipid through upregulating the expressions of ATGL, HSL, PPARγ, C/EBPα and PPARα in adipose tissue of the mice. In differentiated 3T3-L1 cells, curcumin reduced glycerol release and increased glucose uptake via upregulating PPARγ and C/EBPα. We concluded that curcumin has potential to improve glycolipid metabolism disorders caused by obesity through regulating PPARγ signaling pathway.
Data from: Range-wide population genomics of the Mexican fruit fly: towards development of pathway analysis tools
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction-site associated DNA sequencing, and then developed and demonstrated a panel of highly-differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genome-wide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly-differentiated SNPs that were able to recreate the genome-wide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
Data from: Identification of glucose kinase dependent and independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics
Members of the soil-dwelling prokaryotic genus Streptomyces are indispensable for the recycling of complex polysaccharides, and produce a wide range of natural products. Nutrient availability is a major determinant for the switch to development and antibiotic production in streptomycetes. Carbon catabolite repression (CCR), a main signaling pathway underlying this phenomenon, was so far considered fully dependent on the glycolytic enzyme glucose kinase (Glk). Here we provide evidence of a novel Glk-independent pathway in Streptomyces coelicolor, using advanced proteomics that allowed the comparison of the expression of some 2,000 proteins, including virtually all enzymes for central metabolism. While CCR and inducer exclusion of enzymes for primary and secondary metabolism and precursor supply for natural products is mostly mediated via Glk, enzymes for the urea cycle, as well as for biosynthesis of the γ-butyrolactone Scb1 and the responsive cryptic polyketide Cpk are subject to Glk-independent CCR. Deletion of glkA led to strong downregulation of biosynthetic proteins for prodigionin and calcium-dependent antibiotic (CDA) in mannitol-grown cultures. Repression of bldB, bldN, and its target bldM explains the poor development of S. coelicolor on solid-grown cultures containing glucose. A new model for carbon catabolite repression in streptomycetes is presented.
Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of ANAC055 (encoding a transcription factor) increased in wild-type Arabidopsis under drought stress. Further analyses showed that CAU1 bound to the promoter of ANAC055 and suppressed its expression via H4R3sme2-type histone methylation in the promoter region. Thus, under drought stress, a decreased level of CAU1 led to an increased transcript level of ANAC055, which induced the expression of P5CS1 and increased proline level independently of CAS. Drought tolerance and the level of proline were found to be decreased in the cau1 anac055 double-mutant, while proline supplementation restored drought sensitivity in the anac055 mutant. Our results reveal the details of a novel pathway leading to drought tolerance mediated by CAU1.
Data from: Selection for population specific adaptation has shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post glacial colonization
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20 % of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during post-glacial colonization of the species.
Data from: One phase of the dormancy developmental pathway is critical for the evolution of insect seasonality
Evolutionary change in the timing of dormancy enables animals and plants to adapt to changing seasonal environments and can result in ecological speciation. Despite its clear biological importance, the mechanisms underlying the evolution of dormancy timing in animals remain poorly understood because of a lack of anatomical landmarks to discern which phase of dormancy an individual is experiencing. Taking advantage of the nearly universal characteristic of metabolic suppression during insect dormancy (diapause), we use patterns of respiratory metabolism to document physiological landmarks of dormancy and test which of the distinct phases of the dormancy developmental pathway contribute to a month-long shift in diapause timing between a pair of incipient moth species. Here, we show that divergence in life cycle between the earlier-emerging E-strain and the later-emerging Z-strain of European corn borer (ECB) is clearly explained by a delay in the timing of the developmental transition from the diapause maintenance phase to the termination phase. Along with recent findings indicating that life-cycle differences between ECB strains stem from allelic variation at a single sex-linked locus, our results demonstrate how dramatic shifts in animal seasonality can result from simple developmental and genetic changes. Although characterizing the multiple phases of the diapause developmental programme in other locally adapted populations and species will undoubtedly yield surprises about the nature of animal dormancy, results in the ECB moth suggest that focusing on genetic variation in the timing of the dormancy termination phase may help explain how (or whether) organisms rapidly respond to global climate change, expand their ranges after accidental or managed introductions, undergo seasonal adaptation, or evolve into distinct species through allochronic isolation.
Data from: Repeated eye reduction events reveal multiple pathways to degeneration in a family of marine snails
Eye reduction occurs in many troglobitic, fossorial, and deep-sea animals but there is no clear consensus on its evolutionary mechanism. Given the highly conserved and pleiotropic nature of many genes instrumental to eye development, degeneration might be expected to follow consistent evolutionary trajectories in closely related animals. We tested this in a comparative study of ocular anatomy in solariellid snails from deep and shallow marine habitats using morphological, histological, and tomographic techniques, contextualized phylogenetically. Of 67 species studied, 15 lack retinal pigmentation and at least seven have eyes enveloped by surrounding epithelium. Independent instances of reduction follow numerous different morphological trajectories. We estimate eye loss has evolved at least seven times within Solariellidae, in at least three different ways: characters such as pigmentation loss, obstruction of eye aperture, and "lens" degeneration can occur in any order. In one instance, two morphologically distinct reduction pathways appear within a single genus, Bathymophila. Even amongst closely related animals living at similar depths and presumably with similar selective pressures, the processes leading to eye loss have more evolutionary plasticity than previously realized. Although there is selective pressure driving eye reduction, it is clearly not morphologically or developmentally constrained as has been suggested by previous studies.
Data from: Catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes in the 'anaerobic' termite gut spirochete Treponema primitia
Microorganisms have evolved a spectacular diversity of metabolisms, some of which allow them to overcome environmental constraints, utilize abundant but inaccessible resources and drive nutrient cycling in various ecosystems. The termite hindgut microbial community is optimized to metabolize wood, and in recent years, the in situ physiological and ecological functions of community members have been researched. Spirochetes are abundant in the termite gut, and herein, putative aromatic meta-cleavage pathway genes typical of aerobic pseudomonads were located in genomes of homoacetogenic termite hindgut 'anaerobes', Treponema primitia str. ZAS-1 and ZAS-2. Phylogenetic analyses suggest the T. primitia catechol 2,3-dioxygenase and several other essential meta-pathway genes were acquired from an α-proteobacterium in the distant past to augment several genes T. primitia acquired from anaerobic firmicutes that do not directly catabolize aromatics but can contribute to the final pathway steps. Further, transcripts for each meta-pathway gene were expressed in strictly anaerobic cultures of T. primitia str. ZAS-2 indicative of constitutive pathway expression. Also, the addition of catechol + O2 to T. primitia liquid cultures resulted in the transient accumulation of trace amounts of the yellow ring cleavage product, hydroxymuconic semialdehyde. This is the first evidence of aromatic ring cleavage in the phylum (division) Spirochetes. Results also support a possible role for T. primitia in termite hindgut O2/lignin aromatic monomer metabolism. Potential O2-dependent yet nonrespiratory microbial metabolisms have heretofore been overlooked and warrant further investigation. These metabolisms could describe the degradation of plant-derived and other aromatics in microoxic environments and contribute significantly to carbon turnover.
Data from: Spartina alterniflora invasion drastically increases methane production potential by shifting methanogenesis from hydrogenotrophic to methylotrophic pathway in a coastal marsh
1. Plant invasion can strongly influence carbon (C) cycling processes, thus it may affect climate change by altering C sequestration and greenhouse gas emissions in the invaded ecosystem. Since 1979, the exotic Spartina alterniflora has rapidly expanded in China's coastal areas, where significant increase in methane (CH4) emissions has been documented from post-invaded sites. However, a mechanistic understanding of the structural and functional changes of associated methanogens accompanying this invasion remains elusive. 2. Here we conducted integrated biogeochemical investigations on methanogenic substrates, activity, and diversity to identify implications of S. alterniflora invasion for methanogenesis in coastal wetlands. To do this, we collected and analyzed 0–50 cm soil profiles from an uncolonized tidal flat (TF) and salt marshes that S. alterniflora has invaded for 1 year (SA-1) and 12 years (SA-12) in Jiangsu, China. Methanogenic community composition was characterized by massive parallel sequencing. The rates and pathways of methanogenesis were determined by adding trace concentrations of 13C-labeled substrates to anaerobic incubated samples. 3. Our results revealed that 12-year invasion of S. alterniflora drastically increased CH4 production potential by one order of magnitude over that of TF. This substantial increase was primarily attributed to methanogenesis from trimethylamine; its rates increased by two orders of magnitude over TF whereas those from acetate and H2/CO2 increased far less. Hydrogenotrophic methanogenesis was the dominant pathway operating in the TF, but methanotrophic pathway contributed most to CH4 production in the surface layer of SA-1 and upper-most 40-cm layers of SA-12. Consistent with these observations, the dominant methanogens shifted from obligate hydrogenotrophic Methanococcales in TF to potential methylamine-utilizing Methanosarcinaceae in SA-12. Our Mantel analysis indicated that 'non-competitive' trimethylamine, derived from cytoplasmic osmolytes of S. alterniflora, was the major driver of this change in methanogenic community composition. 4. Synthesis. Our results suggest that invasive S. alterniflora plants gradually facilitated the local dominance of methylotrophic Methanosarcinaceae by changing the key type of methanogenic substrate in coastal marshes. Shifts in methanogen communities and enhanced availability of trimethylamine elevated the rates and importance of methylotrophic methanogenesis, thereby markedly increasing CH4 production potential and emission rates in this type of ecosystem.
Data from: Pathways to fitness: carry-over effects of late hatching and urbanisation on lifetime mating success
Life history theory and most empirical studies assume carry-over effects of larval conditions to shape adult fitness through their impact on metamorphic traits (age and mass at metamorphosis). Yet, very few formal tests of this connection across metamorphosis exist, because this entails longitudinal studies from the egg stage and requires measuring fitness in (semi)natural conditions. In a longitudinal one-year common-garden rearing experiment consisting of an outdoor microcosm part for the larval stage and a large outdoor insectary part for the adult stage, we studied the effects of two factors related to time constraints in the larval stage (egg hatching period and urbanisation) on life history traits and lifetime mating success in the males of the damselfly Coenagrion puella. We reared early- and late-hatched larvae from each of three rural and three urban populations from the egg stage throughout their adult life. Key findings were that both the hatching period and urbanisation shaped adult fitness, yet through different pathways. As expected, the more time-constrained late-hatched individuals accelerated their larval life history and this was associated with a lower lifetime mating success. A path analysis revealed this carry-over effect was mediated by the changes in the two metamorphic traits (reduced age and lower mass at emergence). Notably, urban males had a 50% lower lifetime mating success, which was not mediated by age and mass at emergence, and possibly driven by their shorter lifespan. Our results point to long-term carry-over effects of the usually ignored natural variation in egg hatching dates, and further contribute to the limited evidence showing fitness costs of adjusting to an urban lifestyle.
Data from: Cyclic population dynamics and density-dependent intransitivity as pathways to coexistence between co-occurring annual plants
1. Recent studies have brought renewed attention to the importance of complex species interactions - notably intransitive interactions - to patterns of plant community diversity. One underappreciated avenue through which intransitivity can occur is through cyclic population dynamics. Though such cyclic intransitive relationships have been extensively studied in predator-prey systems, evidence of their importance in competitive communities, notably plant communities, is more limited. Most studies of coexistence in plant communities assume fixed-point coexistence even while utilizing models that allow for cyclic population dynamics. 2. In this paper, we explore the potential for density-dependent, cyclic population dynamics and intransitivity in a model for annual plants. We then examine how these density-dependent cycles impact mutual invasibility and ultimately stable coexistence between plant species pairs. We do this using data collected from four co-occurring annual plant species living in natural wildflower communities in SW Western Australia. To maximize the number of biologically plausible pathways by which coexistence mediated by density-dependent cyclic intransitivity can occur, we use an annual plant model that allows for competitive direct interactions, facilitative direct interactions, and higher-order interactions between species. 3. Results from our empirically-parameterized model suggest that monocultures of all four focal species can have cyclic solutions with periodicity greater than 1 under sunny ("open") or shaded field conditions. Cyclic patterns drive variation in annual abundance patterns, with stable solutions for persistent monocultures and invasibility potential (the capacity of one population to invade another) common. Mutual invasibility in the face of cyclic population dynamics was found for just one of six species pairs, only under open environmental conditions. Our results illustrate the potential for cyclic intransitivity to both drive and prevent stable coexistence in environmentally heterogeneous biological communities. 4. Synthesis. We provide analytical and empirical evidence that coexistence in competitive communities (annual plants) can be achieved under non-equilibrium circumstances, through density-dependent cyclic intransitivity. Our results suggest that cyclic population dynamics may be common and important for coexistence dynamics in some types of communities. In such communities, the exploration of stable coexistence should therefore include consideration of cyclic as well as fixed-point equilibria for maximal accuracy.
Data from: Prednisolone induces osteoporosis-like phenotypes via focal adhesion signaling pathway in zebrafish larvae
Patients taking glucocorticoid or glucocorticoid-like drugs for an extended period of time may develop osteoporosis, termed glucocorticoid-induced osteoporosis (GIOP). GIOP is the most common form of secondary osteoporosis, but the mechanism underlying its development is unclear. In the present study, we used prednisolone to treat zebrafish larvae to investigate GIOP. Our RNA deep-sequencing (RNA-seq) results show that prednisolone affects genes known to act in the extracellular region. Therefore the extracellular region, extracellular matrix, and collagen trimer might be involved in glucocorticoid-induced osteoporosis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the focal adhesion signaling pathway is the most enriched signaling pathway in terms of differentially expressed genes (DEGs). In this pathway, integrin subunit alpha 10 (itga10) and integrin subunit beta like 1 (itgbl1), genes encoding two adapter proteins, were down-regulated in the prednisolone-treated larvae. Further experiments showed that prednisolone contributes to GIOP by down-regulating itga10 and itgbl1.
Data from: The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluskan herbivores
Although slugs and snails play important roles in terrestrial ecosystems and cause considerable damage on a variety of crop plants, knowledge about the mechanisms of plant immunity to mollusks is limited. We found slugs to be natural herbivores of Arabidopsis thaliana and therefore investigated possible resistance mechanisms of this species against several molluskan herbivores. Treating wounded leaves with the mucus residue ("slime trail") of the Spanish slug Arion lusitanicus increased wound-induced jasmonate levels, suggesting the presence of defense elicitors in the mucus. Plants deficient in jasmonate biosynthesis and signaling suffered more damage by molluskan herbivores in the laboratory and in the field, demonstrating that JA-mediated defenses protect A. thaliana against slugs and snails. Furthermore, experiments using A. thaliana mutants with altered levels of specific glucosinolate classes revealed the importance of aliphatic glucosinolates in defending leaves and reproductive structures against mollusks. The presence in mollusk feces of known and novel metabolites arising from glutathione conjugation with glucosinolate hydrolysis products suggests that molluskan herbivores actively detoxify glucosinolates. Higher levels of aliphatic glucosinolates were found in plants during the night compared to the day, which correlated well with the nocturnal activity rhythms of slugs and snails. Our data highlight the function of well-known anti-herbivore defense pathways in resistance against slugs and snails and suggest an important role for the diurnal regulation of defense metabolites against nocturnal molluskan herbivores.
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
Background: Functional magnetic resonance imaging (fMRI) is an advanced and frequently used technique for studying brain functions in humans and increasingly so in animals. A key element of analyzing fMRI data is group analysis, for which valid spatial normalization is a prerequisite. In the current study we applied normalization and group analysis to a dataset from an auditory functional MRI experiment in anesthetized beagles. The stimulation paradigm used in the experiment was composed of simple Gaussian noise and regular interval sounds (RIS), which included a periodicity pitch as an additional sound feature. The results from the performed group analysis were compared with those from single animal analysis. In addition to this, the data were examined for brain regions showing an increased activation associated with the perception of pitch. Results: With the group analysis, significant activations matching the position of the right superior olivary nucleus, lateral lemniscus and internal capsule were identified, which could not be detected in the single animal analysis. In addition, a large cluster of activated voxels in the auditory cortex was found. The contrast of the RIS condition (including pitch) with Gaussian noise (no pitch) showed a significant effect in a region matching the location of the left medial geniculate nucleus. Conclusion: By using group analysis additional activated areas along the canine auditory pathways could be identified in comparison to single animal analysis. It was possible to demonstrate a pitch-specific effect, indicating that group analysis is a suitable method for improving the results of auditory fMRI studies in dogs and extending our knowledge of canine neuroanatomy.
Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations
Understanding how diversity emerges in a single niche is not fully understood. Rugged fitness landscapes and epistasis between beneficial mutations could explain coexistence amongst emerging lineages. To provide an experimental test of this notion, we investigated epistasis amongst four pleiotropic mutations in rpoS, mglD, malT and hfq present in two coexisting lineages that repeatedly fixed in experimental populations of Escherichia coli. The mutations were transferred into the ancestral background individually or in combination of double or triple alleles. The combined competitive fitness of two or three beneficial mutations from the same lineage was consistently lower than the sum of the competitive fitness of single mutants – a clear indication of negative epistasis within lineages. We also found sign epistasis (i.e. the combined fitness of two beneficial mutations lower than the ancestor), not only from two different lineages (i.e. hfq and rpoS) but also from the same lineage (i.e. mglD and malT). The sign epistasis between loci of different lineages indeed indicated a rugged fitness landscape, providing an epistatic explanation for the coexistence of distinct rpoS and hfq lineages in evolving populations. The negative and sign epistasis between beneficial mutations within the same lineage can further explain the order of mutation acquisition.
Data from: Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid-based plumage colouration
Many color ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of color elaboration are condition-dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid-based plumage coloration, one of the best-known condition-dependent ornaments, color elaboration stems from both condition-dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here we tested whether multiple color components may be condition-dependent, by using a comprehensive 3 x 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of coloration. Plumage coloration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid-deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition-dependent pathways, affected by different sources of variation, determine color elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.
Data from: Rab6 is required for multiple apical transport pathways but not the basolateral transport pathway in Drosophila photoreceptors
Polarized membrane trafficking is essential for the construction and maintenance of multiple plasma membrane domains of cells. Highly polarized Drosophila photoreceptors are an excellent model for studying polarized transport. A single cross-section of Drosophila retina contains many photoreceptors with 3 clearly differentiated plasma membrane domains: a rhabdomere, stalk, and basolateral membrane. Genome-wide high-throughput ethyl methanesulfonate screening followed by precise immunohistochemical analysis identified a mutant with a rare phenotype characterized by a loss of 2 apical transport pathways with normal basolateral transport. Rapid gene identification using whole-genome resequencing and single nucleotide polymorphism mapping identified a nonsense mutation of Rab6 responsible for the apical-specific transport deficiency. Detailed analysis of the trafficking of a major rhabdomere protein Rh1 using blue light-induced chromophore supply identified Rab6 as essential for Rh1 to exit the Golgi units. Rab6 is mostly distributed from the trans-Golgi network to a Golgi-associated Rab11-positive compartment that likely recycles endosomes or transport vesicles going to recycling endosomes. Furthermore, the Rab6 effector, Rich, is required for Rab6 recruitment in the trans-Golgi network. Moreover, a Rich null mutation phenocopies the Rab6 null mutant, indicating that Rich functions as a guanine nucleotide exchange factor for Rab6. The results collectively indicate that Rab6 and Rich are essential for the trans-Golgi network–recycling endosome transport of cargoes destined for 2 apical domains. However, basolateral cargos are sorted and exported from the trans-Golgi network in a Rab6-independent manner.
Data from: De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways
Background: Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth. Results: The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future. Conclusions: Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.
Data from: Opening the tap: increased riverine connectivity strengthens marine food web pathways.
Reduction of ecosystem connectivity has long-lasting impacts on food webs. Anadromous fish, which migrate from marine to freshwater ecosystems to complete reproduction, have seen their historically larger ecosystem role undercut by widespread riverine habitat fragmentation and other impacts mainly derived from anthropogenic sources. The result has been extensive extirpations and increased susceptibility to a suite of environmental factors that currently impede recovery. Under this present-day context of reduced productivity and connectivity, aggressive management actions and enforcement of catch limits including bycatch caps and complete moratoria on harvest have followed. What remains less understood are the implications of changes to food webs that co-occurred. What benefits restoration could provide in terms of ecosystem functioning in relation to economic costs associated with dam removal and remediation is unknown and can limit the scope and value of restoration activities. Here we employ, historical landscape-based biomass estimates of anadromous alosine for the first time in an ecosystem modeling of the Northeast US large marine ecosystem (LME), to evaluate the value of improving connectivity by measuring the increase in energy flow and population productivity. We compared a restored alosine model to a contemporary model, analyzing the impacts of the potential increase of connectivity between riverine and oceanic systems. We observed changes in ecosystem functional structure and widespread ecosystem benefits for fisheries and conservation efforts. A key advantage was the potential for a 26% biomass increase of piscivorous with high economic value, including Atlantic cod, and for a 69% increase for species of conservation concern such as pelagic sharks, seabirds and marine mammals. Our study highlights the benefits of increased connectivity between freshwater and ocean ecosystems. We demonstrate the significant role anadromous forage fish could play in improving specific fisheries and overall ecosystem functioning, mainly through the diversification of species capable of transferring primary production to upper trophic levels, adding to benefits associated with their restoration.
Data from: An alternative pathway to eusociality: exploring the molecular and functional basis of fortress defense
Some animals express a form of eusociality known as 'fortress defense', in which defense rather than brood care is the primary social act. Aphids are small plant-feeding insects, but like termites, some species express division of labor and castes of aggressive juvenile 'soldiers'. What is the functional basis of fortress defense eusociality in aphids? Previous work showed that the acquisition of venoms might be a key innovation in aphid social evolution. We show that the lethality of aphid soldiers derives in part from the induction of exaggerated immune responses in insects they attack. Comparisons between closely-related social and non-social species identified a number of secreted effector molecules that are candidates for immune modulation, including a convergently-recruited protease described in unrelated aphid species with venom-like functions. These results suggest that aphids are capable of antagonizing conserved features of the insect immune response, and provide new insights into the mechanisms underlying the evolution of fortress defense eusociality in aphids.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.