miRNome expression analysis in canine diffuse large B-cell lymphoma.

Introduction: Lymphoma is a common canine cancer with translational relevance to human disease. Diffuse large B-cell lymphoma (DLBCL) is the most frequent subtype, contributing to almost fifty percent of clinically recognized lymphoma cases. Identifying new biomarkers capable of early diagnosis and monitoring DLBCL is crucial for enhancing remission rates. This research seeks to advance our knowledge of the molecular biology of DLBCL by analyzing the expression of microRNAs, which regulate gene expression by negatively impacting gene expression via targeted RNA degradation or translational repression. The stability and accessibility of microRNAs make them appropriate biomarkers for the diagnosis, prognosis, and monitoring of diseases. Methods: We extracted and sequenced microRNAs from ten fresh-frozen lymph node tissue samples (six DLBCL and four non-neoplastic). Results: Small RNA sequencing data analysis revealed 35 differently expressed miRNAs (DEMs) compared to controls. RT-qPCR confirmed that 23/35 DEMs in DLBCL were significantly upregulated (n = 14) or downregulated (n = 9). Statistical significance was determined by comparing each miRNA's average expression fold-change (2-Cq) between the DLCBL and healthy groups by applying the unpaired parametric Welch's 2-sample t-test and false discovery rate (FDR). The predicted target genes of the DEMs were mainly enriched in the PI3K-Akt-MAPK pathway. Discussion: Our data point to the potential value of miRNA signatures as diagnostic biomarkers and serve as a guideline for subsequent experimental studies to determine the targets and functions of these altered miRNAs in canine DLBCL.

Pulmonary and neurological health effects associated with exposure to representative composite manufacturing emissions and corresponding alterations in circulating metabolite profiles.

Cured-in-place pipe (CIPP) technology is increasingly being utilized to repair aging and damaged pipes, however, there are concerns associated with the public health hazards of emissions. CIPP installation involves the manufacture of a new plastic composite pipe at the worksite and includes multiple variable components including resin material, curing methods, and operational conditions. We hypothesize styrene-based composite manufacturing emissions (CMEs) will induce greater pulmonary inflammatory responses and oxidative stress, as well as neurological toxicity compared with nonstyrene CMEs. Further, these CME-toxicological responses will be sex- and time-dependent. To test the hypothesis, representative CMEs were generated using a laboratory curing chamber and characterized using thermal desorption-gas chromatography-mass spectrometry and photoionization detector. Styrene was released during staying, isothermal curing, and cooling phases of the process and peaked during the cooling phase. Male and female C57BL6/J mice were utilized to examine alterations in pulmonary responses and neurotoxicity 1 day and 7 days following exposure to air (controls), nonstyrene-CMEs, or styrene-CMEs. Serum styrene metabolites were increased in mice exposed to styrene-CMEs. Metabolic and lipid profiling revealed alterations related to CIPP emissions that were resin-, time-, and sex-dependent. Exposure to styrene-CMEs resulted in an influx of lymphocytes in both sexes. Expression of inflammatory and oxidative stress markers, including Tnfα, Vcam1, Ccl2, Cxcl2, Il6, Cxcl1, Tgfß1, Tgmt2, and Hmox1, displayed alterations following exposure to emissions. These changes in pulmonary and neurological markers of toxicity were dependent on resin type, sex, and time. Overall, this study demonstrates resin-specific differences in representative CMEs and alterations in toxicity endpoints, which can potentially inform safer utilization of composite manufacturing processes.

MicroRNA Biomarkers in Canine Diffuse Large B-Cell Lymphoma.

Lymphoma is among the most common cancer in dogs. Diffuse large B-cell lymphoma (DLBCL) is the predominant type, accounting for up to half of all cases. Definitive diagnosis of DLBCL relies on cytologic evaluation with immunophenotyping, or histopathology and immunohistochemistry when needed. A rapid and specific molecular test aiding in the diagnosis could be beneficial. Noncoding microRNAs (miRNAs) are regulators of gene expression involved in a variety of cellular processes, including cell differentiation, cell cycle progression, and apoptosis. Not surprisingly, miRNA expression is aberrant in diseases such as cancers. Their high stability and abundance in tissues make them promising biomarkers for diagnosing and monitoring diseases. This study aimed to identify miRNA signatures of DLBCL to develop ancillary molecular diagnostic tools. miRNA was isolated from formalin-fixed, paraffin-embedded lymph node tissue from 22 DLBCL and 14 nonneoplastic controls. Relative gene expression of 8 tumor-regulating miRNAs was achieved by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction). The results showed downregulation of the let-7 family of miRNAs and miR-155, whereas miR-34a was upregulated in DLBCL compared to the controls. We demonstrated that the combination of expression levels of miR-34a and let-7f or of let-7b and let-7f achieved 100% differentiation between DLBCL and controls. Furthermore, let-7f alone discriminated DLBCL from nonneoplastic tissue in 97% of cases. Our results represent one step forward in search of a rapid and accurate ancillary diagnostic test for DLBCL in dogs.

Consequences of intraspecific variation in seed dispersal for plant demography, communities, evolution and global change.

As the single opportunity for plants to move, seed dispersal has an important impact on plant fitness, species distributions and patterns of biodiversity. However, models that predict dynamics such as risk of extinction, range shifts and biodiversity loss tend to rely on the mean value of parameters and rarely incorporate realistic dispersal mechanisms. By focusing on the mean population value, variation among individuals or variability caused by complex spatial and temporal dynamics is ignored. This calls for increased efforts to understand individual variation in dispersal and integrate it more explicitly into population and community models involving dispersal. However, the sources, magnitude and outcomes of intraspecific variation in dispersal are poorly characterized, limiting our understanding of the role of dispersal in mediating the dynamics of communities and their response to global change. In this manuscript, we synthesize recent research that examines the sources of individual variation in dispersal and emphasize its implications for plant fitness, populations and communities. We argue that this intraspecific variation in seed dispersal does not simply add noise to systems, but, in fact, alters dispersal processes and patterns with consequences for demography, communities, evolution and response to anthropogenic changes. We conclude with recommendations for moving this field of research forward.

Forecasting effects of tree species reintroduction strategies on carbon stocks in a future without historical analog.

American chestnut (Castanea dentata) was once an important component forests in the central Appalachians (USA), but it was functionally extirpated nearly a century ago. Attempts are underway to reintroduce blight-resistant chestnut to its former range, but it is uncertain how current forest composition, climate, and atmospheric changes and disturbance regimes will interact to determine future forest dynamics and ecosystem services. The combination of novel environmental conditions (e.g. climate change), a reintroduced tree species and new disturbance regimes (e.g. exotic insect pests, fire suppression) have no analog in the past that can be used to parameterize phenomenological models. We therefore used a mechanistic approach within the LANDIS-II forest landscape model that relies on physiological first principles to project forest dynamics as the outcome of competition of tree cohorts for light and water as a function of temperature, precipitation, CO2 concentration, and life history traits. We conducted a factorial landscape simulation experiment to evaluate specific hypotheses about future forest dynamics in two study sites in the center of the former range of chestnut. Our results supported the hypotheses that climate change would favor chestnut because of its optimal temperature range and relative drought resistance, and that chestnut would be less competitive in the more mesic Appalachian Plateau province because competitors will be less stressed. The hypothesis that chestnut will increase carbon stocks was supported, although the increase was modest. Our results confirm that aggressive restoration is needed regardless of climate and soils, and that increased aggressiveness of chestnut restoration increased biomass accumulation. The hypothesis that chestnut restoration will increase both compositional and structural richness was not supported because chestnut displaced some species and age cohorts. Although chestnut restoration did not markedly enhance carbon stocks, our findings provide hope that this formerly important species can be successfully reintroduced and associated ecosystem services recovered.

Eastern gray squirrels are consistent shoppers of seed traits: insights from discrete choice experiments.

Seeds of many hardwood trees are dispersed by scatter-hoarding rodents, and this process is often mediated by the traits of seeds. Although numerous studies have linked seed traits to seed preference by rodents, little is known about how rodents forage for seeds when multiple desirable and undesirable seed traits are available simultaneously. Here, we adopt a novel method of designing choice experiments to study how eastern gray squirrels (Sciurus carolinensis) select for 6 traits (caloric value, protein content, tannin concentration, kernel mass, dormancy period and toughness of shell) among seeds. From n = 426 seed-pair presentations, we found that squirrels preferentially consumed seeds with short dormancy or tougher shells, and preferentially cached seeds with larger kernel mass, tougher shells and higher tannin concentrations. By incorporating random effects, we found that squirrels exhibited consistent preferences for seed traits, which is likely due to the fitness consequences associated with maintaining cached resources. Furthermore, we found that squirrels were willing to trade between multiple traits when caching seeds, which likely results in more seed species being cached in the fall. Ultimately, our approach allowed us to compute the relative values of different seed traits to squirrels, despite covariance among studied traits across seed species. In addition, by investigating how squirrels trade among different seed traits, important insights can be gleaned into behavioral mechanisms underlying seed caching (and, thus, seed survival) dynamics as well as evolutionary strategies adopted by plants to attract seed dispersers. We describe how discrete choice experiments can be used to study resource selection in other ecological systems.

Seed fate and decision-making processes in scatter-hoarding rodents.

A mechanistic understanding of seed movement and survival is important both for the development of theoretical models of plant population dynamics, spatial spread, and community assembly, and for the conservation and management of plant communities under global change. While models of wind-borne seed dispersal have advanced rapidly over the past two decades, models for animal-mediated dispersal have failed to make similar progress due to their dependence on interspecific interactions and complex, context-dependent behaviours. In this review, we synthesize the literature on seed dispersal and consumption by scatter-hoarding, granivorous rodents and outline a strategy for development of a general mechanistic seed-fate model in these systems. Our review decomposes seed dispersal and survival into six distinct sub-processes (exposure, harvest, allocation, preparation, placement, and recovery), and identifies nine intermediate (latent) variables that link physical state variables (e.g. seed and animal traits, habitat structure) to decisions regarding seed allocation to hoarding or consumption, cache placement and management, and deployment of radicle-pruning or embryo excision behaviours. We also highlight specific areas where research on these intermediate relationships is needed to improve our mechanistic understanding of scatter-hoarder behaviour. Finally, we outline a strategy to combine detailed studies on individual functional relationships with seed-tracking experiments in an iterative, hierarchical Bayesian framework to construct, refine, and test mechanistic models for context-dependent, scatter-hoarder-mediated seed fate.

Vegetative and Adaptive Traits Predict Different Outcomes for Restoration Using Hybrids.

Hybridization has been implicated as a driver of speciation, extinction, and invasiveness, but can also provide resistant breeding stock following epidemics. However, evaluating the appropriateness of hybrids for use in restoration programs is difficult. Past the F1 generation, the proportion of a progenitor's genome can vary widely, as can the combinations of parental genomes. Detailed genetic analysis can reveal this information, but cannot expose phenotypic alterations due to heterosis, transgressive traits, or changes in metabolism or development. In addition, because evolution is often driven by extreme individuals, decisions based on phenotypic averages of hybrid classes may have unintended results. We demonstrate a strategy to evaluate hybrids for use in restoration by visualizing hybrid phenotypes across selected groups of traits relative to both progenitor species. Specifically, we used discriminant analysis to differentiate among butternut (Juglans cinerea L.), black walnut (J. nigra L.), and Japanese walnut (J. ailantifolia Carr. var. cordiformis) using vegetative characters and then with functional adaptive traits associated with seedling performance. When projected onto the progenitor trait space, naturally occurring hybrids (J. × bixbyi Rehd.) between butternut and Japanese walnut showed introgression toward Japanese walnut at vegetative characters but exhibited a hybrid swarm at functional traits. Both results indicate that hybrids have morphological and ecological phenotypes that distinguish them from butternut, demonstrating a lack of ecological equivalency that should not be carried into restoration breeding efforts. Despite these discrepancies, some hybrids were projected into the space occupied by butternut seedlings' 95% confidence ellipse, signifying that some hybrids were similar at the measured traits. Determining how to consistently identify these individuals is imperative for future breeding and species restoration efforts involving hybrids. Discriminant analysis provides a useful technique to visualize past selection mechanisms and current variation in hybrid populations, especially when key ecological traits that distinguish progenitors are unknown. Furthermore, discriminant analysis affords a tool to assess ecological equivalency of hybrid populations and breeding program efforts to select for certain traits and monitor the amount of variability of those traits, relative to progenitors.

Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions.

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27-73%), and combined effects of seed traits and phylogeny of hardwood trees (5-55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 "global" axes of traits that were phylogenetically autocorrelated at the family and genus level and a third "local" axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30-76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.

Mast species composition alters seed fate in North American rodent-dispersed hardwoods.

Interactions between plants and scatter-hoarding animals may shift from mutualism to predation as a function of the resources available to those animals. Because seed species differ in their nutrient content and defenses to predation, resource selection and cache management by scatter-hoarders, and thus seed fate, may also depend on the relative availability of different seed types. We tracked the fates of tagged Castanea dentata, Quercus alba, and Q. rubra seeds presented to rodents in pairwise combinations and found that C. dentata, which has moderate dormancy prior to germination, survived better in the presence of Q. alba (no dormancy) than with Q. rubra (longer dormancy). Decisions made by scatter-hoarders in response to the composition of available seed resources can alter the relationship between masting and seed dispersal effectiveness in individual tree species and may have influenced the evolution of asynchrony among species-specific masting patterns in temperate forests. In theory, preferential allocation of certain seed species to storage or consumption could also result in indirect apparent predation by one seed species on another.

Does multiple seed loading in Blue Jays result in selective dispersal of smaller acorns?

Studies from both tropical and temperate systems show that scatter-hoarding rodents selectively disperse larger seeds farther from their source than smaller seeds, potentially increasing seedling establishment in larger-seeded plants. Size-biased dispersal is evident in many oaks (Quercus) and is true both across and within species. Here, we predict that intraspecifc variation in seed size also influences acorn dispersal by the Blue Jay (Cyanocitta cristata Linnaeus), but in an opposite manner. Blue Jays are gape-limited and selectively disperse smaller acorn species (e.g. pin oaks [Quercus palustris Münchh]), but often carry several acorns in their crop during a single dispersal event. We predict that jays foraging on smaller acorns will load more seeds per trip and disperse seeds to greater distances than when single acorns are carried in the bill. To test this, we presented free-ranging Blue Jays with pin oak acorns of different sizes over a 2-year period. In each of 16 experimental trials, we monitored the birds at a feeding station with remote cameras and determined the number of acorns removed and the distance acorns were dispersed when cached. Jays were significantly more likely to engage in multiple seed loading with smaller seeds in both years of the study. During the second year, these smaller acorns were dispersed farther than larger acorns, and during the first year, larger acorns were dispersed farther, revealing an inconsistent response to seed size during our study. We suggest that in some circumstances, multiple seed loading by Blue Jays may favor dispersal in some plant species.

Do Dispersing Monkeys Follow Kin? Evidence from Gray-cheeked Mangabeys (Lophocebus albigena).

Among social vertebrates, immigrants may incur a substantial fitness cost when they attempt to join a new group. Dispersers could reduce that cost, or increase their probability of mating via coalition formation, by immigrating into groups containing first- or second-degree relatives. We here examine whether dispersing males tend to move into groups containing fathers or brothers in gray-cheeked mangabeys (Lophocebus albigena) in Kibale National Park, Uganda. We sampled blood from 21 subadult and adult male mangabeys in 7 social groups and genotyped them at 17 microsatellite loci. Twelve genotyped males dispersed to groups containing other genotyped adult males during the study; in only 1 case did the group contain a probable male relative. Contrary to the prediction that dispersing males would follow kin, relatively few adult male dyads were likely first- or second-degree relatives; opportunities for kin-biased dispersal by mangabeys appear to be rare. During 4 yr of observation, adult brothers shared a group only once, and for only 6 wk. Mean relatedness among adult males sharing a group was lower than that among males in different groups. Randomization tests indicate that closely related males share groups no more often than expected by chance, although these tests had limited power. We suggest that the demographic conditions that allow kin-biased dispersal to evolve do not occur in mangabeys, may be unusual among primates, and are worth further attention.

Selection ratios on community aggregated traits estimate ecological filters imposed on species by sites.

Variation in community structure is mediated by interactions between species traits and a site's environmental characteristics. Previously, data on community composition at sites has been employed to correlate trait and environmental variables (e.g., RLQ analysis) and to predict community-level expression of quantitative traits (i.e., community aggregated traits). Here, we demonstrate that the selection ratio, a method originating in animal resource selection studies, can estimate the ecological filters that site conditions impose on species traits by combining observed community aggregated traits with null models of species availability. This flexible, nonparametric approach expresses the filter at each site as a probability density function for the selection of individuals possessing a given trait value. By doing so, it generalizes the community aggregated trait concept to include categorical as well as continuous traits and allows for both intraspecific variation in trait expression and differences in species availability among sites. The resulting site-level filter functions can be related to environmental covariates by standard statistical approaches (e.g., regression). The method complements existing techniques for analyzing trait-environment interactions in community ecology.