Interannual, seasonal, and diel variation in soil respiration relative to ecosystem respiration at a wetland to upland slope at Harvard Forest

Soil carbon dioxide efflux (soil respiration, SR) was measured with eight autochambers at two locations along a wetland to upland slope at Harvard Forest over a 4 year period, 2003–2007. SR was consistently higher in the upland plots than at the wetland margin during the late summer/early fall. Seasonal and diel hystereses with respect to soil temperatures were of sufficient magnitude to prevent quantification of the influence of soil moisture, although apparent short‐term responses of SR to precipitation occurred. Calculations of annual cumulative SR illustrated a decreasing trend in SR over the 5 year period, which were correlated with decreasing springtime mean soil temperatures. Spring soil temperatures decreased despite rising air temperatures over the same period, possibly as an effect of earlier leaf expansion and shading. The synchronous decrease in spring soil temperatures and SR during regional warming of air temperatures may represent a negative feedback on a warming climate by reducing CO2 production from soils. SR reached a maximum later in the year than total ecosystem respiration (ER) measured at a nearby eddy covariance flux tower, and the seasonality of their temperature response patterns were roughly opposite. SR, particularly in the upland, exceeded ER in the late summer/early fall in each year, suggesting that areas of lower efflux such as the wetland may be significant in the flux tower footprint or that long‐term bias in either estimate may create a mismatch. Annual estimates of ER decreased over the same period and were highly correlated with SR

A new model of Holocene peatland net primary production, decomposition, water balance, and peat accumulation

Peatland carbon and water cycling are tightly coupled, so dynamic modeling of peat accumulation over decades to millennia should account for carbon-water feedbacks. We present initial results from a new simulation model of long-term peat accumulation, evaluated at a wellstudied temperate bog in Ontario, Canada. The Holocene Peat Model (HPM) determines vegetation community composition dynamics and annual net primary productivity based on peat depth (as a proxy for nutrients and acidity) and water table depth. Annual peat (carbon) accumulation is the net balance above- and below-ground productivity and litter/peat decomposition – a function of peat hydrology (controlling depth to and degree of anoxia). Peat bulk density is simulated as a function of degree of humification, and affects the water balance through its influence on both the growth rate of the peat column and on peat hydraulic conductivity and the capacity to shed water. HPM output includes both time series of annual carbon and water fluxes, peat height, and water table depth, as well as a final peat profile that can be “cored” and compared to field observations of peat age and macrofossil composition. A stochastic 8500-yr, annual precipitation time series was constrained by a published Holocene climate reconstruction for southern Quebec. HPM simulated 5.4 m of ´ peat accumulation (310 kg C m−2 ) over 8500 years, 6.5% of total NPP over the period. Vascular plant functional types accounted for 65% of total NPP over 8500 years but only 35% of the final (contemporary) peat mass. Simulated age-depth and carbon accumulation profiles were compared to a radiocarbon dated 5.8 m, c.9000-yr core. The simulated core was younger than observations at most depths, but had a similar overall trajectory; carbon accumulation rates were generally higher in the simulation and were somewhat more variable than observations. HPM results were sensitive to centuryscale anomalies in precipitation, with extended drier periods (precipitation reduced ∼10%) causing the peat profile to lose carbon (and height), despite relatively small changes in NP

Host genetic control of gut microbiome composition.

The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships

Discovery of a Role for Rab3b in Habituation and Cocaine Induced Locomotor Activation in Mice Using Heterogeneous Functional Genomic Analysis

Substance use disorders are prevalent and present a tremendous societal cost but the mechanisms underlying addiction behavior are poorly understood and few biological treatments exist. One strategy to identify novel molecular mechanisms of addiction is through functional genomic experimentation. However, results from individual experiments are often noisy. To address this problem, the convergent analysis of multiple genomic experiments can discern signal from these studies. In the present study, we examine genetic loci that modulate the locomotor response to cocaine identified in the recombinant inbred (BXD RI) genetic reference population. We then applied the GeneWeaver software system for heterogeneous functional genomic analysis to integrate and aggregate multiple studies of addiction genomics, resulting in the identification o

QTL and systems genetics analysis of mouse grooming and behavioral responses to novelty in an open field

International audienceThe open field is a classic test used to assess exploratory behavior, anxiety, and locomotor activity in rodents. Here we mapped quantitative trait loci (QTLs) underlying behaviors displayed in an open field, using a panel of 53 BXD recombinant inbred mouse strains with deep replication (10 per strain and sex). The use of these strains permits the integration and comparison of data obtained in different laboratories, and also offers the possibility to study trait covariance by exploiting powerful bioinformatics tools and resources. We quantified behavioral traits during 20 min test sessions including (1) percent time spent and distance travelled near the wall (thigmotaxis), (2) leaning against the wall, (3) rearing, (4) jumping, (5) grooming duration, (6) grooming frequency, (7) locomotion, and (8) defecation. All traits exhibit moderate heritability making them amenable to genetic analysis. We identified a significant QTL on chromosome M.m. 4 at ~104 Mb that modulates grooming duration in both males and females (LRS values of ~18, explaining 25% and 14% of the variance, respectively) and a suggestive QTL modulating locomotion that maps to the same locus. Bioinformatic analysis indicates Disabled 1 (Dab1, a key protein in the reelin signaling pathway) as a particularly strong candidate gene modulating these behaviors. We also found two highly suggestive QTLs for a sex by strain interaction for grooming duration on chromosomes 13 and 17. In addition, we identified a pairwise epistatic interaction between loci on chromosomes 12 at 36-37 Mb and 14 at 34-36 Mb that influences rearing frequency in males

Integration of heterogeneous functional genomics data in gerontology research to find genes and pathway underlying aging across species.

Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world\u27s population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data from functional genomics studies of aging. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and applied to several questions in genrontology using. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan

Relationship between ecosystem productivity and photosynthetically-active radiation for northern peatlands

We analyzed the relationship between net ecosystem exchange of carbon dioxide (NEE) and irradiance (as photosynthetic photon flux density or PPFD), using published and unpublished data that have been collected during midgrowing season for carbon balance studies at seven peatlands in North America and Europe. NEE measurements included both eddy-correlation tower and clear, static chamber methods, which gave very similar results. Data were analyzed by site, as aggregated data sets by peatland type (bog, poor fen, rich fen, and all fens) and as a single aggregated data set for all peatlands. In all cases, a fit with a rectangular hyperbola (NEE = α PPFD Pmax/(α PPFD + Pmax) + R) better described the NEE-PPFD relationship than did a linear fit (NEE = β PPFD + R). Poor and rich fens generally had similar NEE-PPFD relationships, while bogs had lower respiration rates (R = −2.0μmol m−2s−1 for bogs and −2.7 μmol m−2s−1 for fens) and lower NEE at moderate and high light levels (Pmax = 5.2 μmol m−2s−1 for bogs and 10.8 μmol m−2s−1 for fens). As a single class, northern peatlands had much smaller ecosystem respiration (R = −2.4 μmol m−2s−1) and NEE rates (α = 0.020 and Pmax = 9.2μmol m−2s−1) than the upland ecosystems (closed canopy forest, grassland, and cropland) summarized by Ruimy et al. [1995]. Despite this low productivity, northern peatland soil carbon pools are generally 5–50 times larger than upland ecosystems because of slow rates of decomposition caused by litter quality and anaerobic, cold soils

Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration.

Genome-wide association studies and other discovery genetics methods provide a means to identify previously unknown biological mechanisms underlying behavioral disorders that may point to new therapeutic avenues, augment diagnostic tools, and yield a deeper understanding of the biology of psychiatric conditions. Recent advances in psychiatric genetics have been made possible through large-scale collaborative efforts. These studies have begun to unearth many novel genetic variants associated with psychiatric disorders and behavioral traits in human populations. Significant challenges remain in characterizing the resulting disease-associated genetic variants and prioritizing functional follow-up to make them useful for mechanistic understanding and development of therapeutics. Model organism research has generated extensive genomic data that can provide insight into the neurobiological mechanisms of variant action, but a cohesive effort must be made to establish which aspects of the biological modulation of behavioral traits are evolutionarily conserved across species. Scalable computing, new data integration strategies, and advanced analysis methods outlined in this review provide a framework to efficiently harness model organism data in support of clinically relevant psychiatric phenotypes

Curating gene sets: challenges and opportunities for integrative analysis.

Genomic data interpretation often requires analyses that move from a gene-by-gene focus to a focus on sets of genes that are associated with biological phenomena such as molecular processes, phenotypes, diseases, drug interactions or environmental conditions. Unique challenges exist in the curation of gene sets beyond the challenges in curation of individual genes. Here we highlight a literature curation workflow whereby gene sets are curated from peer-reviewed published data into GeneWeaver (GW), a data repository and analysis platform. We describe the system features that allow for a flexible yet precise curation procedure. We illustrate the value of curation by gene sets through analysis of independently curated sets that relate to the integrated stress response, showing that sets curated from independent sources all share significant Jaccard similarity. A suite of reproducible analysis tools is provided in GW as services to carry out interactive functional investigation of user-submitted gene sets within the context of over 150 000 gene sets constructed from publicly available resources and published gene lists. A curation interface supports the ability of users to design and maintain curation workflows of gene sets, including assigning, reviewing and releasing gene sets within a curation project context