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Fetal alcohol exposure can lead to developmental abnormalities, intellectual disability, and behavioral changes, collectively termed fetal alcohol spectrum disorder (FASD). In 2015, the Centers for Disease Control found that 1 in 10 pregnant women report alcohol use and more than 3 million women in the USA are at risk of exposing their developing fetus to alcohol. Drosophila melanogaster is an excellent genetic model to study developmental effects of alcohol exposure because many individuals of the same genotype can be reared rapidly and economically under controlled environmental conditions. Flies exposed to alcohol undergo physiological and behavioral changes that resemble human alcohol-related phenotypes. Here, we show that adult flies that developed on ethanol-supplemented medium have decreased viability, reduced sensitivity to ethanol, and disrupted sleep and activity patterns. To assess the effects of exposure to alcohol during development on brain gene expression, we performed single cell RNA sequencing and resolved cell clusters with differentially expressed genes which represent distinct neuronal and glial populations. Differential gene expression showed extensive sexual dimorphism with little overlap between males and females. Gene expression differences following developmental alcohol exposure were similar to previously reported differential gene expression following cocaine consumption, suggesting that common neural substrates respond to both drugs. Genes associated with glutathione metabolism, lipid transport, glutamate and GABA metabolism, and vision feature in sexually dimorphic global multi-cluster interaction networks. Our results provide a blueprint for translational studies on alcohol-induced effects on gene expression in the brain that may contribute to or result from FASD in human populations. [ABSTRACT FROM AUTHOR]

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We studied the reproductive attributes (reproductive phenology, pollination and seed dispersion) of understory woody species from a rainforest area in the Araripe‐Apodi National Forest (FLONA), NE Brazil. The FLONA has a representative number of fauna and flora species that are important for the local climatic, hydrological and ecological equilibrium of the region. The community was composed of 68 species distributed in 43 genera and 26 plant families. Melastomataceae was the family with the highest species richness. Most species (61.76%) shared floral traits that promoted bee pollination, for example white, dish type, medium‐sized flowers with pollen as the main resource. Zoochory was the most frequent dispersion system (76.47%), followed by autochory (16.17%) and anemochory (7.35%). Resource distribution (flowers and fruits) was uniform throughout the year, and pollination and dispersion networks were significantly modular, composed of five and four modules, respectively. In the pollination network, bees occurred in almost all modules, but flies, hummingbirds, butterflies and hawk moths were more restricted to certain modules, partially highlighting the idea of pollination syndromes. In the dispersion network, the modules were composed of birds from different families; only one module was comprised of all sampled mammals. Our results show that most species depend on the action of biotic vectors during their reproductive processes (pollination and dispersal). Those interactions are fundamental for maintaining biological diversity in different tropical ecosystems. [ABSTRACT FROM AUTHOR]

A more complete picture of the function of plants in ecosystems results from understanding biotic interactions and this study examined the interactions between ferns and foliicolous lichens. A sampling method involving 15-h walks in each of two tropical forests in Brazil was employed to assess foliicolous lichen diversity on ferns. The nature of foliicolous lichen-fern interactions, and their relationship with forest types (lowland and submontane) and leaf traits (hairs and leaf area), was investigated. Eleven fern species were found to be hosts to 30 foliicolous lichen taxa. Telmatoblechnum serrulatum and Meniscium longifolium were considered the key hosts harboring a greater number (18 and 12) of lichen taxa, of which five taxa were restricted to these two ferns. Approximately 55% of the foliicolous lichens were found on a single fern host. Thicharia sp. A and Gyalectidium filicinum were the more interactive taxa, occurring on seven and ten host ferns, respectively. The forest type had no influence on the interactions. The foliicolous lichen-host fern network differed significantly from null expectations, and there was no sign of specialization. There was also no variation related to the presence of hairs on the sampled ferns (80% had glabrous leaves) and leaf hairs had no significant influence on lichen diversity. Furthermore, leaf area had no influence on the diversity of lichen species. Our results provide a first picture of diversity of foliicolous lichens on fern assemblages in tropical forests. However, there are uncertainties about the mechanisms driving these interactions so more research is needed. [ABSTRACT FROM AUTHOR]

[Display omitted] • South Africa and Argentina share basic motifs engraved on ostrich and rhea eggshells. • These engraving practices were more frequent during the mid-Holocene's drier climate. • Rhea eggshell flasks ceased to be used during the final Late Holocene. • Imagery engraved on rhea eggshells continued to be expressed on other materials. • Ostrich eggshell flasks continued in use until the present, although engraved less frequently. • Engraved designs reduced the risk of inhabiting unpredictable environments. We compare motifs engraved on ostrich and rhea eggshell fragments from southern Africa and southern South America respectively. These elements were part of water flasks used, transported and cached by hunter-gatherers. We define trends in the motifs engraved on eggshells, inquire about their temporal and spatial distribution, their diversity and their information content in the context of the social interactions and boundaries developed among mobile peoples. A typology of basic motifs occurring on each side of the Atlantic was built to perform a three-step analysis. The first evaluates motif composition through three periods that we name 'middle', 'initial late' and 'final late' Holocene, the second examines image circulation within each period and the third assesses the information content of the engravings. Even though the ostrich and rhea eggshells' visual repertoires are similar, motif variability and motif spatial distribution between the periods analyzed present differences related to the particular social processes that took place in each region. Ostrich eggshells' higher information content could imply that interaction networks in southern Africa were more extensive than in southern South America. However, sample bias could also be affecting the results obtained. [ABSTRACT FROM AUTHOR]

Abstract Background Abdominal fat is the major adipose tissue in chickens. The growth status of abdominal fat during postnatal late development ultimately affects meat yield and quality in chickens. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that regulate gene expression at the post-transcriptional level. Studies have shown that miRNAs play an important role in the biological processes involved in adipose tissue development. However, few studies have investigated miRNA expression profiles and their interaction networks associated with the postnatal late development of abdominal adipose tissue in chickens. Results We constructed four small RNA libraries from abdominal adipose tissue obtained from Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 507 known miRNAs and 53 novel miRNAs were identified based on the four small RNA libraries. Fifty-one significant differentially expressed (SDE) miRNAs were identified from six combinations by comparative analysis, and the expression patterns of these SDE miRNAs were divided into six subclusters by cluster analysis. Gene ontology enrichment analysis showed that the SDE miRNAs were primarily involved in the regulation of fat cell differentiation, regulation of lipid metabolism, regulation of fatty acid metabolism, and unsaturated fatty acid metabolism in the lipid metabolism- or deposition-related biological process categories. In addition, we constructed differentially expressed miRNA–mRNA interaction networks related to abdominal adipose development. The results showed that miRNA families, such as mir-30, mir-34, mir-199, mir-8, and mir-146, may have key roles in lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens. Conclusions This study determined the dynamic miRNA transcriptome and characterized the miRNA–mRNA interaction networks in Gushi chicken abdominal adipose tissue for the first time. The results expanded the number of known miRNAs in abdominal adipose tissue and provide novel insights and a valuable resource to elucidate post-transcriptional regulation mechanisms during postnatal late development of abdominal adipose tissue in chicken.

Environmental filtering, spatial factors and species interactions are fundamental ecological mechanisms for community organisation, yet the role of such interactions across different environmental and spatial settings remains mostly unknown. In this study, we investigated fish community organisation scenarios and seasonal species-to-species associations potentially reflecting biotic associations along the Qiupu River (China). Based on a latent variable approach and a tree-based method, we compared the relative contribution of the abiotic environment, spatial covariates and potential species associations for variation in the community structure, and assessed whether different assembly scenarios were modulated by concomitant changes in the interaction network structure of fish communities across seasons. We found that potential species associations might have been underestimated in community-based assessments of stream fish. Omnivore species, since they have more associations with other species, were found to be key components sustaining fish interaction networks across different stream orders. Hence, we suggest that species interactions, such as predation and competition, likely played a key role in community structure. For instance, indices accounting for network structure, such as connectance and nestedness, were strongly correlated with the unexplained residuals from our latent variable approach, thereby re-emphasising that biotic signals, potentially reflecting species interactions, may be of primary importance in determining stream fish communities across seasons. Overall, our findings indicate that interaction network structures are a powerful tool to reflect the contribution of potential species associations to community assembly. From an applied perspective, this study should encourage freshwater ecologists to empirically capture and manage biotic constraints in stream ecosystems across different geographical and environmental settings, especially in the context of the ever-increasing impacts of human-induced local extinction debts and species invasions.

Background Plant-pollinator mutualistic networks show non-random structural properties that promote species coexistence. However, these networks show high variability in the interacting species and their connections. Mismatch between plant and pollinator attributes can prevent interactions, while trait matching can enable exclusive access, promoting pollinators’ niche partitioning and, ultimately, modularity. Thus, plants belonging to specialized modules should integrate their floral traits to optimize the pollination function. Herein, we aimed to analyze the biological processes involved in the structuring of plant-hummingbird networks by linking network morphological constraints, specialization, modularity and phenotypic floral integration. Methods We investigated the understory plant-hummingbird network of two adjacent habitats in the Lacandona rainforest of Mexico, one characterized by lowland rainforest and the other by savanna-like vegetation. We performed monthly censuses to record plant-hummingbird interactions for 2 years (2018–2020). We also took hummingbird bill measurements and floral and nectar measurements. We summarized the interactions in a bipartite matrix and estimated three network descriptors: connectance, complementary specialization (H2’), and nestedness. We also analyzed the modularity and average phenotypic floral integration index of each module. Results Both habitats showed strong differences in the plant assemblage and network dynamics but were interconnected by the same four hummingbird species, two Hermits and two Emeralds, forming a single network of interaction. The whole network showed low levels of connectance (0.35) and high specialization (H2’ = 0.87). Flower morphologies ranged from generalized to specialized, but trait matching was an important network structurer. Modularity was associated with morphological specialization. The Hermits Phaethornis longirostris and P. striigularis each formed a module by themselves, and a third module was formed by the less-specialized Emeralds: Chlorestes candida and Amazilia tzacatl. The floral integration values were higher in specialized modules but not significantly higher than that formed by generalist species. Conclusions Our findings suggest that biological processes derived from both trait matching and “forbidden” links, or nonmatched morphological attributes, might be important network drivers in tropical plant-hummingbird systems while morphological specialization plays a minor role in the phenotypic floral integration. The broad variety of corolla and bill shapes promoted niche partitioning, resulting in the modular organization of the assemblage according to morphological specialization. However, more research adding larger datasets of both the number of modules and pollination networks for a wider region is needed to conclude whether phenotypic floral integration increases with morphological specialization in plant-hummingbird systems.

Aim: Global changes will redistribute biodiversity, reshaping ecological interactions and ecosystem processes. The decoupling in the distribution of plants and their mutualistic seed dispersers, for instance, may have overlooked eco‐evolutionary effects. How animal‐dispersed plants will respond to changes in the distribution of their seed dispersers remains largely an open question. Here, we forecast the consequences of climate change and frugivory interactions for the spatial distribution and seed size evolution of a Neotropical palm species. Location: Atlantic forests of South America. Time period: Present day, end of 21st century. Major taxa studied: Thirty‐two species of frugivorous birds, and a palm (Euterpe edulis). Methods: Future patterns of animal–plant co‐occurrence were derived from ecological niche models, climate forecasts, projections of future forest loss, and seed dispersal simulations. We further explored the evolutionary effect of the spatial reorganization of interactions by modelling palm seed sizes as a function of changes in the distribution of frugivore traits. Results: Our models indicate that future climate change and deforestation may reduce the palm's suitable distribution by 20%–50%. However, our simulations suggest that 66% of all remaining future suitable distribution (76,200 km2) would still be inaccessible to the palm without the active dispersal of seeds by frugivores. In addition, novel frugivore communities are projected to have smaller mean body mass and gape size (−23% and −10%, respectively), due to the loss of large frugivores, which may translate into a 6%–17% reduction of seed sizes across the palm's remaining distribution. Main conclusions: Our projections indicate that frugivore seed dispersal may be critical to allow occupancy of future habitat by animal‐dispersed plants. However, loss of large frugivores may affect trait selection regimes, creating hotspots of plant evolution towards smaller seeds. We argue that such complex dynamics emerging from species‐specific responses to global change may reshape the distribution and evolution of several interacting partners worldwide. [ABSTRACT FROM AUTHOR]

Background: Within tropical shallow-water coral reefs, marine sponges provide microhabitats for a wide range of fauna. Although there have been numerous studies and reports of symbiotic relationships amongst sponges and their associated fauna, those pieces of information are isolated and disconnected. For this reason, based on the available literature, we compiled a species-interaction dataset of coral reef marine sponge-associated fauna known to date. New information: We introduce a dataset that includes 67 literature items that report 101 species of sponge hosts clustered in 12 Orders having a host/guest interaction with 284 guest species from six Phyla present in the Northwestern Tropical Atlantic coral reefs. This dataset consists of two types of information: 1. Machine-readable data and 2. Human-readable data. These two types of coding improve the scope of the dataset and facilitate the link between machine platforms and human-friendly displays. We also created an interactive visualisation of the species-interactions dataset and of a dynamic Chord Diagram of the host-guest species connections to generate a user-friendly link between the user and the dataset. [ABSTRACT FROM AUTHOR]

Researchers worldwide with great endeavor searching and repurpose drugs might be potentially useful in fighting newly emerged coronavirus. These drugs show inhibition but also show side effects and complications too. On December 27, 2020, 80,926,235 cases have been reported worldwide. Specifically, in Pakistan, 471,335 has been reported with inconsiderable deaths. Identification of COVID-19 drugs pathway through drug-gene and gene−gene interaction to find out the most important genes involved in the pathway to deal with the actual cause of side effects beyond the beneficent effects of the drugs. The medicines used to treat COVID-19 are retrieved from the Drug Bank. The drug-gene interaction was performed using the Drug Gene Interaction Database to check the relation between the genes and the drugs. The networks of genes are developed by Gene MANIA, while Cytoscape is used to check the active functional association of the targeted gene. The developed systems cross-validated using the EnrichNet tool and identify drug genes' concerned pathways using Reactome and STRING. Five drugs Azithromycin, Bevacizumab, CQ, HCQ, and Lopinavir, are retrieved. The drug-gene interaction shows several genes that are targeted by the drug. Gene MANIA interaction network shows the functional association of the genes like co-expression, physical interaction, predicted, genetic interaction, co-localization, and shared protein domains. Our study suggests the pathways for each drug in which targeted genes and medicines play a crucial role, which will help experts in-vitr o overcome and deal with the side effects of these drugs, as we find out the in-silico gene analysis for the COVID-19 drugs. [ABSTRACT FROM AUTHOR]

Biotic interactions and mutualisms in particular have an important role in ecosystem structure and functioning as well as in the maintenance of biodiversity. Understanding how communities respond to the introduction of non-native species and what determines the establishment of novel interactions between native and introduced species will help in determining the potential impacts of biological invasions. The aims of this work were to assess patterns of frugivory and fruit removal in environments with invasion of non-native fleshy-fruited plants and to evaluate whether novel associations between native frugivores and non-native plants are determined by fruit traits. For this we selected eight study sites in areas with different degrees of invasion of non-native fleshy-fruited plants. In each site, we measured fruit availability and fruit traits of native and non-native plants. In addition, we conducted direct frugivory observations. We found that native and non-native fruits differed based on morphological trait variables, such as fruit weight and dimensions. Only two birds, Elaenia albiceps (smaller and migrant) and Turdus falcklandii (bigger and resident), are the main frugivorous present in the area. At the scale of the community of frugivores, neither visit nor fruit removal rates differ between natives and non-natives. However, at the species scale, while E. albiceps preferentially foraged on native plants, T. falcklandii preferred non-natives. Thus, some generalist frugivorous species like T. falcklandii can play a key role in promoting the invasion of non-native plants. [ABSTRACT FROM AUTHOR]

Background: Plant-pollinator mutualistic networks show non-random structural properties that promote species coexistence. However, these networks show high variability in the interacting species and their connections. Mismatch between plant and pollinator attributes can prevent interactions, while trait matching can enable exclusive access, promoting pollinators' niche partitioning and, ultimately, modularity. Thus, plants belonging to specialized modules should integrate their floral traits to optimize the pollination function. Herein, we aimed to analyze the biological processes involved in the structuring of plant-hummingbird networks by linking network morphological constraints, specialization, modularity and phenotypic floral integration. Methods: We investigated the understory plant-hummingbird network of two adjacent habitats in the Lacandona rainforest of Mexico, one characterized by lowland rainforest and the other by savanna-like vegetation. We performed monthly censuses to record plant-hummingbird interactions for 2 years (2018-2020). We also took hummingbird bill measurements and floral and nectar measurements. We summarized the interactions in a bipartite matrix and estimated three network descriptors: connectance, complementary specialization (H2'), and nestedness. We also analyzed the modularity and average phenotypic floral integration index of each module. Results: Both habitats showed strong differences in the plant assemblage and network dynamics but were interconnected by the same four hummingbird species, two Hermits and two Emeralds, forming a single network of interaction. The whole network showed low levels of connectance (0.35) and high specialization (H2' = 0.87). Flower morphologies ranged from generalized to specialized, but trait matching was an important network structurer. Modularity was associated with morphological specialization. The Hermits Phaethornis longirostris and P. striigularis each formed a module by themselves, and a third module was formed by the less-specialized Emeralds: Chlorestes candida and Amazilia tzacatl. The floral integration values were higher in specialized modules but not significantly higher than that formed by generalist species. Conclusions: Our findings suggest that biological processes derived from both trait matching and "forbidden" links, or nonmatched morphological attributes, might be important network drivers in tropical plant-hummingbird systems while morphological specialization plays a minor role in the phenotypic floral integration. The broad variety of corolla and bill shapes promoted niche partitioning, resulting in the modular organization of the assemblage according to morphological specialization. However, more research adding larger datasets of both the number of modules and pollination networks for a wider region is needed to conclude whether phenotypic floral integration increases with morphological specialization in plant-hummingbird systems. [ABSTRACT FROM AUTHOR]

Assemblages of Neotropical frugivorous bats are structured as a function of the fruit diets of species; however, ecological relationships among closely related species largely remain unknown. This study evaluated the trophic relations among three species of Carollia in a premontane forest of central Peru. To accomplish this, we first determined the diet composition of frugivorous bats to build a bat–fruit interaction network. We then assessed the trophic structure of the bat assemblage using a modularity analysis in the network. Carollia brevicauda and Carollia perspicillata were grouped apart from Carollia benkeithi. This partition occurred because the diet of C. benkeithi was more specialized, characterized by two Piper species, a Cyclanthaceae species, and Banara guianensis. Moreover, C. benkeithi , in contrast to its congeners, did not consume fruits of Ficus or Cecropia (canopy resources). This result and available information on the ecology of Carollia species suggest that small species of Carollia are more likely to carry out most of their feeding activities in the understory than are large species of the genus. [ABSTRACT FROM AUTHOR]

The ecological dynamics of co‐flowering communities are largely mediated by pollinators. However, current understanding of pollinator‐mediated interactions primarily relies on how co‐flowering plants influence attraction of shared pollinators, and much less is known about plant–plant interactions that occur via heterospecific pollen (HP) transfer. Invaded communities in particular can be highly affected by the transfer of alien pollen, but the strength, drivers and fitness consequences of these interactions at a community scale are not well understood.Here we analyse HP transfer networks in nine coastal communities in the Yucatan Mexico that vary in the relative abundance of invasive flowers to evaluate how HP donation and receipt varies between native and alien plants. We further evaluate whether HP donation and receipt are mediated by floral traits (e.g. display, flower size) or pollinator visitation rate. Finally, we evaluated whether post‐pollination success (proportion of pollen tubes produced) was affected by alien HP receipt and whether the effect varied between native and alien recipients.HP transfer networks exhibit relatively high connectance (c. 15%), suggesting high HP transfer within the studied communities. Significant network nestedness further suggests the existence of species that predominantly act as HP donors or recipients in the community. Species‐level analyses showed that natives receive 80% more HP compared to alien species, and that alien plants donate 40% more HP than natives. HP receipt and donation were mediated by different floral traits and such effects were independent of plant origin (native or alien). The proportion of alien HP received significantly affected conspecific pollen tube success in natives, but not that of alien species.Synthesis. Our results suggest that HP transfer in invaded communities is widespread, and that native and alien species play different roles within HP transfer networks, which are mediated by a different suite of floral traits. Alien species, in particular, play a central role as HP donors and are more tolerant to HP receipt than natives—a finding that points to two overlooked mechanisms facilitating alien plant invasion and success within native co‐flowering communities. [ABSTRACT FROM AUTHOR]

Despite evidence that seasonal variation may lead to the persistence of competing species, studies on the effect of seasonality on community network structures are sparse. Identifying whether seasonal network changes are the result of turnover or rewiring (i.e. rearrangement of interactions among species), also remains understudied in multi‐trophic communities. Using species abundance data for 38 species over three years (from nine sites across central/eastern United States) and a novel tree‐based inference method, we constructed seasonal networks for a multi‐trophic freshwater stream fish community. We found that seasonality influences species interactions, particularly through rewiring (81%) as compared to species turnover (19%). Moreover, the number of rewiring interactions was best explained by fish status as a piscivore/non‐piscivore and species maximum length (R2 = 0.41). Our findings suggest that rewiring may be a dominant process in stream fish communities experiencing seasonal environments and that traits linked to trophic‐level could be a good indicator of a species contribution to rewiring. As networks dominated by rewiring may be more robust, this network approach could be a valuable conservation tool for identifying which biological relationships must be retained for communities to avoid extinction. [ABSTRACT FROM AUTHOR]

There are ubiquitous microorganisms in the rhizosphere forming symbiosis with host plants. Some of them, including plant growth promoting rhizobacteria, arbuscular mycorrhizal fungi, non-clavicipitaceous endo-phytes and ectomycorrhizal fungi, play important roles in improving plant nutrition status and alleviating the damage caused by drought, flooding, salinity and heavy metal stress. This paper reviewed the underlying mechanisms of enhancing plant chromium (Cr) tolerance by these four groups of rhizosphere microorganisms. As a whole, they can directly or indirectly improve plant Cr tolerance via various and different functions including promoting plant growth, reducing the Cr bioavailability, decreasing the translocation of metal from roots to shoots, stabilizing metal by fungal structures and so on. However, the physiological and molecular mechanisms underlying Cr behavior and detoxification in rhizosphere remain largely unknown. It's also of great importance to clarify the effect of interaction networks between the rhizosphere microorganisms. [ABSTRACT FROM AUTHOR]

The six mammalian glycosaminoglycans (GAGs), chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate, are linear polysaccharides. Except for hyaluronan, they are sulfated to various extent, and covalently attached to proteins to form proteoglycans. GAGs interact with growth factors, morphogens, chemokines, extracellular matrix proteins and their bioactive fragments, receptors, lipoproteins, and pathogens. These interactions mediate their functions, from embryonic development to extracellular matrix assembly and regulation of cell signaling in various physiological and pathological contexts such as angiogenesis, cancer, neurodegenerative diseases, and infections. We give an overview of GAG–protein interactions (i.e., specificity and chemical features of GAG- and protein-binding sequences), and review the available GAG–protein interaction networks. We also provide the first comprehensive draft of the GAG interactome composed of 832 biomolecules (827 proteins and five GAGs) and 932 protein–GAG interactions. This network is a scaffold, which in the future should integrate structures of GAG–protein complexes, quantitative data of the abundance of GAGs in tissues to build tissue-specific interactomes, and GAG interactions with metal ions such as calcium, which plays a major role in the assembly of the extracellular matrix and its interactions with cells. This contextualized interactome will be useful to identify druggable GAG–protein interactions for therapeutic purpose: [ABSTRACT FROM AUTHOR]

Marine ecosystems are prone to tipping points, particularly in coastal zones where dramatic changes are associated with interactions between cumulative stressors (e.g., shellfish harvesting, eutrophication and sediment inputs) and ecosystem functions. A common feature of many degraded estuaries is elevated turbidity that reduces incident light to the seafloor, resulting from multiple factors including changes in sediment loading, sea‐level rise and increased water column algal biomass. To determine whether cumulative effects of elevated turbidity may result in marked changes in the interactions between ecosystem components driving nutrient processing, we conducted a large‐scale experiment manipulating sediment nitrogen concentrations in 15 estuaries across a national‐scale gradient in incident light at the seafloor. We identified a threshold in incident light that was related to distinct changes in the ecosystem interaction networks (EIN) that drive nutrient processing. Above this threshold, network connectivity was high with clear mechanistic links to denitrification and the role of large shellfish in nitrogen processing. The EIN analyses revealed interacting stressors resulting in a decoupling of ecosystem processes in turbid estuaries with a lower capacity to denitrify and process nitrogen. This suggests that, as turbidity increases with sediment load, coastal areas can be more vulnerable to eutrophication. The identified interactions between light, nutrient processing and the abundance of large shellfish emphasizes the importance of actions that seek to manage multiple stressors and conserve or enhance shellfish abundance, rather than actions focusing on limiting a single stressor. [ABSTRACT FROM AUTHOR]

Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.

Summary: Accumulation of diverse types of omics data on schizophrenia (SCZ) requires a systems approach to model the interplay between genome, transcriptome, and proteome. We introduce Markov affinity-based proteogenomic signal diffusion (MAPSD), a method to model intra-cellular protein trafficking paradigms and tissue-wise single-cell protein abundances. MAPSD integrates multi-omics data to amplify the signals at SCZ risk loci with small effect sizes, and reveal convergent disease-associated gene modules in the brain. We predicted a set of high-confidence SCZ risk loci followed by characterizing the subcellular localization of proteins encoded by candidate SCZ risk genes, and illustrated that most are enriched in neuronal cells in the cerebral cortex as well as Purkinje cells in the cerebellum. We demonstrated how the identified genes may be involved in neurodevelopment, how they may alter SCZ-related biological pathways, and how they facilitate drug repurposing. MAPSD is applicable in other polygenic diseases and can facilitate our understanding of disease mechanisms. The Bigger Picture: Proteins constitute the functional machinery in a cell. Genetic aberrations may cause disrupting the normal functionality of the proteins. On the other hand, biophysical and biochemical properties of proteins vary in distinct tissues mandating separate modeling of proteomic features given the tissue being studied, e.g. brain in case of schizophrenia. Using the concept of signal diffusion in graph theory, we proposed a model, termed MAPSD, which enables us to leverage proteomic properties of different tissues at single cell resolution along with genomic and epigenomic features of a disease in order to predict potential risk genes which cannot be annotated using common univariate approaches. Taking this approach helps create novel therapeutic hypotheses for precision medicine so that more effective treatments with less side effects on other organs can be developed. Application of MAPSD is not restricted to schizophrenia and most of complex diseases can benefit from the method.

Background Interactions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985–1986 with that in 2016–2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015). Methods The fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985–1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016–2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices. Results We found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016–2017 were either the least connected in the original network (1985–1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016–2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016–2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events. Conclusions Most of the parameters describing the hummingbird-plant network structure remained unchanged after 30 years, with the exception of an increase in plant robustness and hummingbird niche overlap. However, the network’s generalist core was affected by the loss of some species. Also, core plant species such as Ipomoea bracteata, Combretum farinosum, and Justicia candicans were found to be important for maintaining the hummingbird-plant interaction network. The temporal perspective of this study provides unique insights into the conservation of plant-hummingbird networks across time and extreme natural events.

Cytokines are multifunctional small proteins that have a vital influence on inflammatory states of tissues and play a role in signalling and cellular control mechanisms. Cytokine expression has primarily been viewed as a form of direct secretion of molecules through an active transportation; however, other forms of active transport such as extracellular vesicles are at play. This is particularly important in stem cells where signalling molecules are key to communication managing the levels of proliferation, migration, and differentiation into mature cells. This study investigated cytokines from intracellular content, direct cellular secretions, and extracellular vesicles from adult adipose-derived stem cells isolated from three distinct anatomical locations: abdomen, thigh, and chin. The cells were cultured investigated using live cell microscopy, cytokine assays, and bioinformatics analysis. The cytokines quantified and examined from each sample type showed a distinct difference between niche areas and sample types. The varying levels of TNF-alpha, IL-6 and IL-8 cytokines were shown to play a crucial role in signalling pathways such as MAPK, ERK1/2 and JAK-STAT in cells. On the other hand, the chemotactic cytokines IL-1rn, Eotaxin, IP-10 and MCP-1 showed the most prominent changes across extracellular vesicles with roles in noncanonical signalling. By examining the local and tangential roles of cytokines in stem cells, their roles in signalling and in regenerative mechanisms may be further understood.

Species' floral traits and flowering times are known to be the major drivers of pollinator‐mediated plant–plant interactions in diverse co‐flowering communities. However, their simultaneous role in mediating plant community assembly and plant–pollinator interactions is still poorly understood. Since not all species flower at the same time, inference of facilitative and competitive interactions based on floral trait distribution patterns should account for fine phenological structure (intensity of flowering overlap) within co‐flowering communities. Such an approach may also help reveal the simultaneous action of competitive and facilitative interactions in structuring co‐flowering communities.Here we used modularity within a co‐flowering network context, as a novel approach to detect convergent and/or over‐dispersed patterns in floral trait distribution and pollinator sharing. Specifically, we evaluate differences in floral trait and pollinator distribution patterns within (high temporal flowering overlap) and among co‐flowering modules (low temporal flowering overlap). We further evaluate the consistency of observed floral trait and pollinator sharing distribution patterns across space (three geographical regions) and time (dry and rainy seasons).We found that floral trait similarity was significantly higher in plant species within co‐flowering modules than in species among them. This suggests pollinator facilitation may lead to floral trait convergence, but only within co‐flowering modules. However, our results also revealed seasonal and spatial shifts in the underlying interactions (facilitation or competition) driving co‐flowering assembly, suggesting that the prevalent dominant interactions are not static.Synthesis. Overall, we provide strong evidence showing that the use of flowering time and floral trait distribution alone may be insufficient to fully uncover the role of pollinator‐mediated interactions in community assembly. Integrating this information along with patterns of pollinator sharing will greatly help reveal the simultaneous action of facilitative and competitive pollinator‐mediated interactions in co‐flowering communities. The spatial and temporal variation in flowering and trait distribution patterns observed further emphasize the importance of adopting a more dynamic view of community assembly processes. [ABSTRACT FROM AUTHOR]

Network approaches provide insight into the complex web of interspecific interactions that structure ecological communities. However, because data on the functional outcomes of ecological networks are very rarely available, the effect of network structure on ecosystem functions, such as seed dispersal, is largely unknown. Here, we develop a new approach that is able to link interaction networks to a trait‐based seed–dispersal model to estimate community‐wide seed dispersal distances. We simulated networks, using a niche model based on size‐matching between plants and birds, that varied in the degree of niche partitioning, i.e. the overlap in interaction partners between coexisting species. We found that community‐wide dispersal distances were longest when networks had low degrees of niche partitioning. We further found that dispersal distances of plant species with small fruits peaked in models without niche partitioning, whereas dispersal distances of medium and large‐fruited plants peaked at low degrees of niche partitioning. Our simulations demonstrate that the degree of niche partitioning between species is an important determinant of the ecological functions derived from ecological networks and that simulation approaches can provide new insights into the relationship between the structural and functional components of ecological networks. [ABSTRACT FROM AUTHOR]

Gregarious arthropods are able to perform collective decision-making when having different options. In this study, we investigate how the sexual group composition and the geometry of the shelters influence the aggregation patterns of Periplaneta americana. We show that groups of males, groups of females and mixed groups composed of males and females have different interactions' networks leading to different collective preferences in symmetrical (two horizontal or two vertical shelters) and asymmetrical (one vertical and one horizontal shelter) conditions that take their origin in the differences in the strengths of interattractions and in individual geotaxis preferences. [ABSTRACT FROM AUTHOR]

Niche breadth is a unifying concept spanning diverse aspects of ecology, evolution, and conservation biology. Niche breadth usually refers to the diversity of resources used or environments tolerated by an individual, population, species, or clade. Here we review key research in ecology, evolution, and conservation biology in light of niche breadth. Namely, we explore the role of niche breadth in shaping geographic distributions and species richness from local to landscape scales, how niche breadth evolves and influences lineage diversification, and its use for understanding species invasions, responses to climate change, vulnerability to extinction, and ecosystem functioning. This diverse literature informs a research agenda that identifies focused needs for further progress: testing the hierarchical nature of niche breadth (e.g., of individuals, populations, and species); quantifying correlations in niche breadth among different niche axes and the role of environmental drivers and organismal constraints in generating these correlations; and evaluating the factors that decouple fundamental and realized niches. We describe how this research agenda could help unify disparate subdisciplines and shed light on key questions in ecology, evolution, and conservation. [ABSTRACT FROM AUTHOR]

Background: Studies on tumor-secreted microRNAs point to a functional role of these in cellular communication and reprogramming of the tumor microenvironment. Uptake of tumor-secreted microRNAs by neighboring cells may result in the silencing of mRNA targets and, in turn, modulation of the transcriptome. Studying miRNAs externalized from tumors could improve cancer patient diagnosis and disease monitoring and help to pinpoint which miRNA-gene interactions are central for tumor properties such as invasiveness and metastasis.Methods: Using a bioinformatics approach, we analyzed the profiles of secreted tumor and normal interstitial fluid (IF) microRNAs, from women with breast cancer (BC). We carried out differential abundance analysis (DAA), to obtain miRNAs, which were enriched or depleted in IFs, from patients with different clinical traits. Subsequently, miRNA family enrichment analysis was performed to assess whether any families were over-represented in the specific sets. We identified dysregulated genes in tumor tissues from the same cohort of patients and constructed weighted gene co-expression networks, to extract sets of co-expressed genes and co-abundant miRNAs. Lastly, we integrated miRNAs and mRNAs to obtain interaction networks and supported our findings using prediction tools and cancer gene databases.Results: Network analysis showed co-expressed genes and miRNA regulators, associated with tumor lymphocyte infiltration. All of the genes were involved in immune system processes, and many had previously been associated with cancer immunity. A subset of these, BTLA, CXCL13, IL7R, LAMP3, and LTB, was linked to the presence of tertiary lymphoid structures and high endothelial venules within tumors. Co-abundant tumor interstitial fluid miRNAs within this network, including miR-146a and miR-494, were annotated as negative regulators of immune-stimulatory responses. One co-expression network encompassed differences between BC subtypes. Genes differentially co-expressed between luminal B and triple-negative breast cancer (TNBC) were connected with sphingolipid metabolism and predicted to be co-regulated by miR-23a. Co-expressed genes and TIF miRNAs associated with tumor grade were BTRC, CHST1, miR-10a/b, miR-107, miR-301a, and miR-454.Conclusion: Integration of IF miRNAs and mRNAs unveiled networks associated with patient clinicopathological traits, and underlined molecular mechanisms, specific to BC sub-groups. Our results highlight the benefits of an integrative approach to biomarker discovery, placing secreted miRNAs within a biological context. [ABSTRACT FROM AUTHOR]

Anthropogenic disturbances are jeopardizing ecosystem functioning globally. Yet, we know very little about the effect of human impacts on ecological processes derived from trophic interactions. By focusing on biodiversity components of consumer and resource organisms, such as the diversity of phylogenetic lineages and the diversity of traits that influence species interactions, it is possible to simultaneously address the responses to disturbances and their effects on processes.Here, we evaluate the consequences of forest loss on the ecological process of frugivory between fleshy‐fruited plants and frugivorous birds. For 2 years, and at 14 sites representing a gradient of forest cover in the Cantabrian Range (N Iberian Peninsula), we monitored fruit and bird abundance, and fruit consumption. We compared the response to forest loss of both plants and birds by assessing the changes in phylogenetic and trait‐based functional diversity in relation to forest cover. We further evaluated how changes in these biodiversity components translate into functional changes by estimating the degree of functional complementarity of plant and bird species.We found different responses of plants and birds to forest loss. The diversity of plant assemblages did not respond to changes in forest cover, whereas bird assemblages markedly lost phylogenetic and trait‐based functional diversity at high levels of forest loss. Functional complementarity of birds was well predicted by phylogenetic and trait‐based functional diversity, but functional complementarity of plants depended exclusively on the diversity of traits.Forest loss filtered avian phylogenetic lineages and traits, and influenced how birds contributed to the frugivory process. These results show how the diversity decay of one trophic level may compromise ecological processes derived from trophic interactions. Therefore, we suggest that a multitrophic response‐effect framework, which includes measures of functional traits, lineages and species functional contributions across trophic levels, may be required to fully understand the ecological consequences of biodiversity decays. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Background: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins, taxa, and metabolites, have been inferred, represented, and visualized via graph theory-based networks. Comparisons of multiple networks can help in identifying variations across different biological systems, thereby providing additional insights. However, while a number of online and stand-alone tools exist for generating, analyzing, and visualizing individual biological networks, the utility to batch process and comprehensively compare multiple networks is limited. Results: Here, we present a graphical user interface (GUI)-based web application which implements multiple network comparison methodologies and presents them in the form of organized analysis workflows. Dedicated comparative visualization modules are provided to the end-users for obtaining easy to comprehend, insightful, and meaningful comparisons of various biological networks. We demonstrate the utility and power of our tool using publicly available microbial and gene expression data. Conclusion: NetConfer tool is developed keeping in mind the requirements of researchers working in the field of biological data analysis with limited programming expertise. It is also expected to be useful for advanced users from biological as well as other domains (working with association networks), benefiting from provided ready-made workflows, as they allow to focus directly on the results without worrying about the implementation. While the web version allows using this application without installation and dependency requirements, a stand-alone version has also been supplemented to accommodate the offline requirement of processing large networks. [ABSTRACT FROM AUTHOR]

Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution. Network sciences are introducing network-based models into all relevant biological fields, notably in microbiology and evolutionary biology. The three core principles of evolution – variation, heredity, and differential fitness – crystalized in the 1970s, still serve as a conceptual benchmark for the theory of evolution by natural selection. Network-based inquiries in microbiology tap into the complexity of the systems of interactions that underscore the evolutionary dynamics of cellular life, thereby augmenting our understanding of the three core principles of evolution. Conversely, the improved understanding of evolutionary dynamics provided by networks informs microbiology in various ways. The network-based understanding of evolution is often considered as anti-Darwinian in spirit, a claim that can be debunked using microbiology. [ABSTRACT FROM AUTHOR]

Wild pollinators are necessary for ensuring plant reproduction, not only among crop fields but also remnant and restored ecosystems. Restoration activities should, therefore, lead to wild pollinator recovery, and thus be monitored to evaluate effects on pollinator diversity and functionality. We assessed bee pollinator functional responses in restoration plantings by creating functional groups (traits: body size, nesting location, sociality, and foraging strategy), comparing their abundance and diversity to that of other habitats (i.e., conserved and degraded primary forest fragments, anthropogenic wetlands, and sugarcane fields), and testing for an effect of source habitat (i.e., primary forest fragments) isolation. We analyzed functional effects on pollen transportation by identifying the pollen grains attached on the bodies of bees; creating plant functional groups with the identified species (traits: habit, successional class, geographic origin, and pollination mode); comparing their frequency, diversity, and interaction network structure among habitats; and searching for key interactions in network modules. In general, the abundance and diversity of bee communities and the frequency and diversity of the interacting plant species in restoration plantings were lower than those in primary forest fragments but higher than those in anthropogenic wetlands and sugarcane fields, suggesting that restoration plantings better enhance bee community recovery and functionality than other disturbed habitats. The interacting bees and plants were also negatively affected by habitat isolation, demonstrating the importance of primary forest fragments to supply bee populations to restored sites. The structure of interaction networks was little affected by habitat change and isolation, but the composition and diversity of functional groups varied significantly. There were more effects on larger bee species with more restricted nesting and floral requirements, and the woody species with which they interact most frequently. We identified key functional groups of bee pollinators that deserve priority for conservation because they play an important role in the pollen transportation of some the most relevant species in remnant forests and restoration plantings and also respond more negatively to habitat disturbances. Restoration efforts should include provisioning of nesting resources and management and conservation of primary forest remnant fragments that represent source habitats for them. [ABSTRACT FROM AUTHOR]

Cities represent humanity's most intense impact on our planet, with more than half of all humans now residing in urban areas. Indeed, urbanization has well‐understood impacts on both individual species and general patterns of biodiversity. However, species do not exist in isolation, but are instead members of complex interaction networks that shape patterns of diversity and influence ecosystem services.Despite the importance of species interaction for creating patterns of diversity, we do not understand how urbanization alters these interactions. Here, we investigate how an interaction network (food web) is reshaped by urbanization.We show that, consistent with theory, cities tend to support less diverse ecological communities, and rare species that interact with few species are particularly sensitive to urbanization. As a result, remnant urban food webs tend to have more interactions per species and greater connectance, creating more integrated interaction networks.We discuss the implications of this food web reshaping for ecological stability, eco‐evolutionary dynamics, and the joining of interaction networks and conservation planning. The role of cities in reshaping interaction networks provides an interesting study of food web (dis)assembly, while also shedding light on new approaches to applied conservation issues. [ABSTRACT FROM AUTHOR]

Mutualistic interactions between plants and pollinators play an essential role in the organization and persistence of biodiversity. The structure of interaction networks mediates the resilience of local communities and ecosystem functioning to environmental changes. Hence, network structure conservation may be more critical for maintaining biodiversity and ecological services than the preservation of isolated species in changing landscapes. Here, we intensively surveyed seven 36 km2 landscapes to empirically investigate the effects of forest loss and landscape configuration on the structure of plant–pollinator networks in understory vegetation of Brazilian Atlantic Forest. Our results indicate that forest loss and isolation affect the structure of the plant–pollinator networks, which were smaller in deforested landscapes, and less specialized as patch isolation increased. Lower nestedness and degree of specialization (Hʹ2) indicated that the remaining plant and bee species tend to be generalists, and many of the expected specialized interactions in the network were already lost. Because generalist species generate a cohesive interaction core in these networks, these simplified networks might be resistant to loss of peripheral species, but may be susceptible to the extinction of the most generalist species. We suggest that such a network pattern is an outcome of landscapes with a few remaining isolated patches of natural habitat. Our results add a new perspective to studies of plant–pollinator networks in fragmented landscapes, showing that those interaction networks might also be used to indicate how changes in natural habitat affect biodiversity and biotic interactions. [ABSTRACT FROM AUTHOR]

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Copyright of Revista del Museo de Antropología is the property of Museo de Antropologia - IDACOR and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background. Interactions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985-1986 with that in 2016-2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015). Methods. The fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985-1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016-2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices. Results. We found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016-2017 were either the least connected in the original network (1985-1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016-2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016-2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events. Conclusions. Most of the parameters describing the hummingbird-plant network structure remained unchanged after 30 years, with the exception of an increase in plant robustness and hummingbird niche overlap. However, the network's generalist core was affected by the loss of some species. Also, core plant species such as Ipomoea bracteata, Combretum farinosum, and Justicia candicans were found to be important for maintaining the hummingbird-plant interaction network. The temporal perspective of this study provides unique insights into the conservation of plant-hummingbird networks across time and extreme natural events. [ABSTRACT FROM AUTHOR]

Based on the limited data available to her at the time, Margaret Lyneis proposed that the transition between the Pueblo II and Pueblo III periods in the Moapa Valley was marked by differences in social organization and subsistence strategies. Since then, additional data have become available from new archival research and excavations, making it possible to more fully investigate the ideas presented by Lyneis. In this paper, the newly-available data are used to re-evaluate the nature of the Pueblo II–III transition, and their implications for understanding the terminal Virgin Branch occupation of the Moapa Valley are considered. [ABSTRACT FROM AUTHOR]

Latrophilins (LPHNs) are adhesion GPCRs that are originally discovered as spider’s toxin receptors, but are now known to be involved in brain development and linked to several neuronal and non-neuronal disorders. Latrophilins act in conjunction with other cell adhesion molecules and may play a leading role in its network organization. Here, we focus on the main protein partners of latrophilins, namely teneurins, FLRTs and contactins and summarize their respective temporal and spatial expression patterns, links to neurodevelopmental disorders as well as their structural characteristics. We discuss how more recent insights into the separate cell biological functions of these proteins shed light on the central role of latrophilins in this network. We postulate that latrophilins control the refinement of synaptic properties of specific subtypes of neurons, requiring discrete combinations of proteins.