Bacterioplankton Community Variation Across River to Ocean Environmental Gradients

Coastal zones encompass a complex spectrum of environmental gradients that each impact the composition of bacterioplankton communities. Few studies have attempted to address these gradients comprehensively. We generated a synoptic, 16S rRNA gene-based bacterioplankton community profile of a coastal zone by applying the fingerprinting technique denaturing gradient gel electrophoresis to water samples collected from the Columbia River, estuary, and plume, and along coastal transects covering 360 km of the Oregon and Washington coasts and extending to the deep ocean (>2,000 m). Communities were found to cluster into five distinct groups based on location in the system (ANOSIM, p < 0.003): estuary, plume, epipelagic, shelf bottom (depth < 150 m), and slope bottom (depth > 650 m). Across all environments, abiotic factors (salinity, temperature, depth) explained most of the community variability (ρ = 0.734). But within each coastal environment, biotic factors explained most of the variability. Thus, structuring physical factors in coastal zones, such as salinity and temperature, define the boundaries of many distinct microbial habitats, but within these habitats variability in microbial communities is explained by biological gradients in primary and secondary productivity.     

Community Trait Distribution Across Environmental Gradients

Ecosystems - Variability in community composition is often attributed to underlying differences in physical environments. However, predator–prey interactions can play an equally important...     

Tooth Size Variation in Assemblages of Tremacyllus (Hegetotheriidae,Notoungulata): Insights into Geographical Gradients,Systematics, and Sexual Dimorphism

Tooth size variation within fossil assemblages can be associated with intra- or interspecific variation, functional, developmental, and geographical factors, and/or sexual dimorphism. Understanding these sources of variation is necessary to develop diagnoses for fossil mammals, where teeth are usually the most frequent remains. Tremacyllus (Ameghino, 1891) (Hegetotheriidae, Notoungulata) is a genus of small-sized herbivorous mammals abundant in late Miocene to Pliocene outcrops of southern South America. Its simplified, euhypsodont dentition and size variability have hampered systematics studies and led, for instance, to an overestimation of the number of species. I analyzed tooth size variations within assemblages of Tremacyllus in a quantitative framework to test three hypotheses: (1) magnitudes of size variation are different among tooth loci and assemblages; (2) tooth size follows a geographical pattern within the analyzed sample (Bergmann’s rule), but is also associated with taxonomy; and (3) there is a correlation between size variation and sexual dimorphism reflected in distinguishable subgroups. Results indicate that patterns of variation might be associated with eruption time and/or functional position. Northwestern forms are larger than southwestern-Pampean ones, not conforming to Bergmann’s rule but revealing a strong influence of latitude. Size differences between assemblages agree with dental features that distinguish T. incipiens and T. impressus, allowing expanded species diagnoses. Two size subgroups might reflect sexual dimorphism in the absence of biostratigraphic or morphological differences between them. This interpretation indicates that northwestern specimens referred to T. diminutus should be referred to T. incipiens.

     

Diversity of Anurans Across Agricultural Ponds in Argentina

We examined the anuran diversity of 31 ponds (30 located on the border of soybean cropland and one within a protected forest) in mid-western Entre Ríos Province (Argentina). Moreover, each species found was characterised with respect to its vertical location. Using principal component (PCA) and canonical correspondence analyses (CCA) we quantified associations between species diversity and habitat and spatial variables. A total of 21 anuran species belonging to four families (Microhylidae, Bufonidae, Leptodactylidae and Hylidae) were detected in ponds surrounded by soybean croplands. PCA generated three principal components, which together explained variation in anuran diversity across the agricultural ponds and control site. Negative values of PC-1 described the smaller ponds with narrower hedgerow and monospecific shore vegetation. PC-2 had high loading on pond depth, and PC-3 had negative loading on air temperature. CCA showed a very strong association between the two data sets. We found all guilds related with pond area. Indeed, we found that arboreal species were recorded in large ponds with higher values of shore vegetation index and presence of wider hedgerow. Moreover, a higher number of terrestrial species was found to relate to large pond areas and greater shore vegetation diversity. Finally, aquatic species were related to pond area, shore vegetation index and depth. Anuran diversity across agricultural ponds of mid-western Entre Ríos Province can be affected by local habitat factors such as reduction in pond size and depth, shore vegetation richness, width of hedgerow and air temperatures. Management of anurans to reverse recent declines will require defining high-quality habitat for individual species or group of species, followed by efforts to retain or restore these aquatic habitat. The maintenance of shore vegetation of ponds and hedgerows may increases the number of species and diversity of anurans within agricultural landscapes.     

Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization

The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.     

Classifying Chimpanzee (Pan troglodytes) Landscapes Across Large-Scale Environmental Gradients in Africa

International Journal of Primatology - Primates are sometimes categorized in terms of their habitat. Although such categorization can be oversimplistic, there are scientific benefits from the...     

Chromosomal Passports Provide New Insights into Diffusion of Emmer Wheat

Emmer wheat, Triticum dicoccon schrank (syn. T. dicoccum (schrank) schÜbl.), is one of the earliest domesticated crops, harboring a wide range of genetic diversity and agronomically valuable traits. The crop, however, is currently largely neglected. We provide a wealth of karyotypic information from a comprehensive collection of emmer wheat and related taxa. In addition to C-banding polymorphisms, we identified 43 variants of chromosomal rearrangements in T. dicoccon; among them 26 (60.4%) were novel. The T7A:5B translocation was most abundant in Western Europe and the Mediterranean. The plant genetic resources investigated here might become important in the future for wheat improvement. Based on cluster analysis four major karyotypic groups were discriminated within the T. dicoccon genepool, each harboring characteristic C-banding patterns and translocation spectra: the balkan, asian, european and ethiopian groups. We postulate four major diffusion routes of the crop and discuss their migration out of the Fertile Crescent considering latest archaeobotanical findings.     

Feeding Motor Patterns in Anurans: Insights from Biomechanical Modeling

During feeding in anurans, the mouth opens while the tongue,which is attached to the mandible at the front of the mouth,rotates forward. Due to the relative simplicity of its anatomyand the complexity of its motion, tongue protraction in frogspresents an ideal system for exploring the neural control ofmultijoint movements. In this study, we used a forward dynamic,rigid body model with four segments and two muscles to investigateopen loop control of tongue protraction in the Australian white-lippedtree frog, Litoria caerulea. Model parameters include the massdistribution, initial position and initial angular velocityof each segment and the anatomy and physiology of each muscle.Model variables include the level of muscle activation at eachtime step and impulsive torques to open and close the mouth.The model gives X,Y coordinates of each segment and joint anglesat each time step as output. The model was tested using scaled,normalized EMG signals and impulsive joint torques to predictthe paths of the lower jaw tip and tongue tip. Predicted pathswere compared to experimentally observed paths using Pearsonproduct-moment correlation coefficients. Simulations demonstratethat the genioglossus muscles likely play a minor role, if any,in determining the trajectory of the tongue in most anurans.Most of the force for tongue protraction comes from angularmomentum transferred to the tongue by the opening jaws. In anurans,tongue protraction is dynamically stable and will occur as longas the musculoskeletal elements are in the correct initial position.     

Changes in Ecosystem Function Across Sedimentary Gradients in Estuaries

The input of terrestrial silt and clay (hereafter mud) into coastal environments can alter sediment grain size distribution affecting the structure and functioning of benthic communities. The relationship between sediment mud content and macrofaunal community structure has been well documented, but not the effects on ecosystem function. In 143 plots from the mid-intertidal sites in 9 estuaries, we measured sediment properties, macrofaunal community composition and fluxes of O₂ and NH₄ ⁺ across the sediment–water interface to derive process-based measures of ecosystem function across the sand–mud gradient. We observed reductions in measures of macrofaunal diversity and decreases in the maximum density of key bioturbating bivalves (Austrovenus stutchburyi and Macomona liliana) with increased mud content. Concurrently, the maximum rates of sediment oxygen consumption (SOC), NH₄ ⁺ efflux (NH₄ ⁺) and biomass standardized gross primary production (GPP_Chl-a ) also decreased with increasing mud content. Environmental predictors explained 34–39% (P = 0.005–0.01) of the total variation in ecosystem function in distance-based linear models. After partitioning out the effect of mud, A. stutchburyi abundance was positively correlated and explained 25 and 23% (P = 0.0001) of the variation of SOC and NH₄ ⁺, respectively. Also, mud content (negatively correlated) and temperature (positively correlated) explained 26% of variability in GPP_Chl-a (P = 0.0001). Our results highlight the importance of increased mud content and the associated reduction in the abundance of strongly interacting key species on the loss of ecosystem function in intertidal sand flats.     

Quantitative Genetic Variation in Body Size of Mice from New Mutations

To measure the amount of new genetic variation in 6-week weight of mice arising each generation from mutation, selection lines derived from an initially inbred strain were maintained for 25 generations. An analysis using an animal model with restricted maximum likelihood was applied to estimate a mutational genetic component of variance for the infinitesimal model of many genes of small effect. Assuming that the inbred base population was at a mutation-drift equilibrium, it is estimated that the heritability for body size has increased by 1.0% per generation, with lower and upper confidence limits of 0.6% and 1.6%, respectively. A model which includes a mutational genetic component of variance fits the data much better than one involving only base population genetic variance. A model with no genetic component fits the data very poorly. An environmental covariance of body size of mother and offspring was included in the model and accounts for 10% of the variance. By using information only from the observed response to selection, the estimated increase in heritability from mutation is 0.3% per generation. These values are higher than published estimates for the increase in variance from spontaneous mutations in bristle traits of Drosophila, for which there are extensive data, but similar to estimates for various skeletal traits in mice.     

Comparative Proteomic Analyses Provide New Insights into Low Phosphorus Stress Responses in Maize Leaves

Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH₂PO₄ (intervention group, −P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P<0.05; ≥1.5-fold) significantly in quantity between the +P and −P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO₂ enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large accumulation of peroxides. Maize has developed many different reactive oxygen species (ROS) scavenging mechanisms to cope with low phosphorus stress, including up-regulating its antioxidant content and antioxidase activity. After being subjected to phosphorus stress over a long period, maize may increase its internal phosphorus utilization efficiency by altering photorespiration, starch synthesis and lipid composition. These results provide important information about how maize responds to low phosphorus stress.     

Peroxisome Size Provides Insights into the Function of Autophagy-related Proteins

Autophagy is a major pathway of intracellular degradation mediated by formation of autophagosomes. Recently, autophagy was implicated in the degradation of intracellular bacteria, whose size often exceeds the capacity of normal autophagosomes. However, the adaptations of the autophagic machinery for sequestration of large cargos were unknown. Here we developed a yeast model system to study the effect of cargo size on the requirement of autophagy-related (Atg) proteins. We controlled the size of peroxisomes before their turnover by pexophagy, the selective autophagy of peroxisomes, and found that peroxisome size determines the requirement of Atg11 and Atg26. Small peroxisomes can be degraded without these proteins. However, Atg26 becomes essential for degradation of medium peroxisomes. Additionally, the pexophagy-specific phagophore assembly site, organized by the dual interaction of Atg30 with functionally active Atg11 and Atg17, becomes essential for degradation of large peroxisomes. In contrast, Atg28 is partially required for all autophagy-related pathways independent of cargo size, suggesting it is a component of the core autophagic machinery. As a rule, the larger the cargo, the more cargo-specific Atg proteins become essential for its sequestration.     

Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment

Cyclic nucleotide-gated (CNG) ion channels are key mediators underlying signal transduction in retinal and olfactory receptors. Genetic defects in CNGA3 and CNGB3, encoding two structurally related subunits of cone CNG channels, lead to achromatopsia (ACHM). ACHM is a congenital, autosomal recessive retinal disorder that manifests by cone photoreceptor dysfunction, severely reduced visual acuity, impaired or complete color blindness and photophobia. Here, we report the first canine models for CNGA3-associated channelopathy caused by R424W or V644del mutations in the canine CNGA3 ortholog that accurately mimic the clinical and molecular features of human CNGA3-associated ACHM. These two spontaneous mutations exposed CNGA3 residues essential for the preservation of channel function and biogenesis. The CNGA3-R424W results in complete loss of cone function in vivo and channel activity confirmed by in vitro electrophysiology. Structural modeling and molecular dynamics (MD) simulations revealed R424-E306 salt bridge formation and its disruption with the R424W mutant. Reversal of charges in a CNGA3-R424E-E306R double mutant channel rescued cGMP-activated currents uncovering new insights into channel gating. The CNGA3-V644del affects the C-terminal leucine zipper (CLZ) domain destabilizing intersubunit interactions of the coiled-coil complex in the MD simulations; the in vitro experiments showed incompetent trimeric CNGA3 subunit assembly consistent with abnormal biogenesis of in vivo channels. These newly characterized large animal models not only provide a valuable system for studying cone-specific CNG channel function in health and disease, but also represent prime candidates for proof-of-concept studies of CNGA3 gene replacement therapy for ACHM patients.     

Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder

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Scombroid Fishes Provide Novel Insights into the Trait/Rate Associations of Molecular Evolution

The study of which life history traits primarily affect molecular evolutionary rates is often confounded by the covariance of these traits. Scombroid fishes (billfishes, tunas, barracudas, and their relatives) are unusual in that their mass-specific metabolic rate is positively associated with body size. This study exploits this atypical pattern of trait variation, which allows for direct tests of whether mass-specific metabolic rate or body size is the more important factor of molecular evolutionary rates. We inferred a phylogeny for scombroids from a supermatrix of molecular and morphological characters and used new phylogenetic comparative approaches to assess the associations of body size and mass-specific metabolic rate with substitution rate. As predicted by the body size hypothesis, there is a negative correlation between body size and substitution rate. However, unexpectedly, we also find a negative association between mass-specific metabolic and substitution rates. These relationships are supported by analyses of the total molecular data, separate mitochondrial and nuclear genes, and individual loci, and they are robust to phylogenetic uncertainty. The molecular evolutionary rates of scombroids are primarily tied to body size. This study demonstrates that groups with novel patterns of trait variation can be particularly informative for identifying which life history traits are the primary factors of molecular evolutionary rates.     

Sexual Size Dimorphism in Anurans: Ontogenetic Determination Revealed by an Across-Species Comparison

Ever since Darwin, why and how sexual size dimorphism (SSD) arises among the animal kingdom has puzzled evolutionary biologists. While comparative analyses focus on ultimate causes of this phenomenon, few attempts have been made to quantify its ontogenetic basis. Here we deal with the latter issue using the skeletochronology-based demographic data gathered from the literature for anurans, a group of indeterminately growing vertebrates typically exhibit female-biased SSD. Both non- and phylogenetically corrected analyses showed (1) SSD was correlated positively with the sex difference in adult mean age but negatively with the corresponding difference in annual growth rate, (2) the sex difference in adult mean age tended to be negatively correlated with that in growth rate, and (3) the sex difference in adult mean age was positively correlated with that in age at maturity. We conclude that in anuran lineages, the degree of SSD bias towards females is mediated by sexual bimaturation: females mature later than males, and thus live longer and attain larger despite growing slower. Stronger fecundity selection benefits to females, despite incurring growth cost, in combination with the benefits to males from increased reproductive opportunities resulting from earlier maturity, should be the primary evolutionary drivers of the typically female-biased SSD.