M89V Sialic Acid Acetyl Esterase (SIAE) and All Other Non-Synonymous Common Variants of This Gene Are Catalytically Normal

Catalytically defective rare variants of Sialic acid Acetyl Esterase (SIAE) have previously been linked to autoimmunity. Studies presented here confirm that the M89V SIAE protein and all other products of common variant alleles of SIAE are catalytically normal. Although overexpressing transfected non-lymphoid cells secrete small amounts of SIAE that can associate with the cell surface, normal human lymphocytes do not exhibit cell surface SIAE, supporting genetic evidence in mice that indicates that this protein functions in a lymphocyte intrinsic manner. Analyses of the plasma proteome also indicate that SIAE is not secreted in vivo. A re-analysis exclusively of catalytically defective rare variant alleles of SIAE in subjects in which this gene was completely sequenced confirmed an association of SIAE with autoimmunity. A subset of catalytically defective rare variant SIAE alleles has previously been typed in a large genotyping study comparing a diverse group of disease subjects and controls; our re-analysis of this data shows that catalytically defective alleles are enriched in disease subjects. These data suggest that SIAE may be associated with autoimmunity and that further study of catalytically defective rare variant SIAE alleles in terms of autoimmune disease susceptibility is strongly warranted.     

Scale dependency and the expression of hierarchical structure in Delphinium patches

Hierarchy theory has provided a valuable conceptual framework for studies of heterogeneity. However, there have been few empirical studies of hierarchical structure and little is known about how hierarchical structure originates or varies among systems. Here, I explore how scale dependency can influence the detection of hierarchical structure. Specifically, I compared how heterogeneity changed with scale in patches of larkspur (Delphinium spp). The distribution of Delphinium nelsonii inflorescences was quite uniform over the range of measured scales (1 m²-2500 m²) and only a single level of patchiness was observed. Aggregations of D. barbeyi inflorescences were much more pronounced and this patchiness was evident at many scales. The number of hierarchical levels and the scales at which patchiness occurred varied both within and between plots of D. barbeyi. Because patchiness was not strongly scale-dependent for either species, discrete patch boundaries and well-defined hierarchical levels were not usually apparent even when multiple scales of patchiness were present. In several cases, the scales of detected patchiness depended on the difference in scale between grain (resolution) and extent. I predict that because of the lack of dominant and strongly scale-dependent processes, microlandscapes such as Delphinium meadows, may be less likely to exhibit well-defined hierarchical structure than larger-scale landscapes, especially those heavily altered by human activities.     

Bi-directional modulation of fast inhibitory synaptic transmission by leptin

The hormone leptin has widespread actions in the CNS. Indeed, leptin markedly influences hippocampal excitatory synaptic transmission and synaptic plasticity. However, the effects of leptin on fast inhibitory synaptic transmission in the hippocampus have not been evaluated. Here, we show that leptin modulates GABA_A receptor-mediated synaptic transmission onto hippocampal CA1 pyramidal cells. Leptin promotes a rapid and reversible increase in the amplitude of evoked GABA_A receptor-mediated inhibitory synaptic currents (IPSCs); an effect that was paralleled by increases in the frequency and amplitude of miniature IPSCs, but with no change in paired pulse ratio or coefficient of variation, suggesting a post-synaptic expression mechanism. Following washout of leptin, a persistent depression (inhibitory long-lasting depression) of evoked IPSCs was observed. Whole-cell dialysis or bath application of inhibitors of phosphoinositide 3 (PI 3)-kinase or Akt prevented leptin-induced enhancement of IPSCs indicating involvement of a post-synaptic PI 3-kinase/Akt-dependent pathway. In contrast, blockade of PI 3-kinase or Akt activity failed to alter the ability of leptin to induce inhibitory long-lasting depression, suggesting that this process is independent of PI 3-kinase/Akt. In conclusion these data indicate that the hormone leptin bi-directionally modulates GABA_A receptor-mediated synaptic transmission in the hippocampus. These findings have important implications for the role of this hormone in regulating hippocampal pyramidal neuron excitability.     

Evaluating atmospheric CO2 inversions at multiple scales over a highly inventoried agricultural landscape

An intensive regional research campaign was conducted by the North American Carbon Program (NACP) in 2007 to study the carbon cycle of the highly productive agricultural regions of the Midwestern United States. Forty‐five different associated projects were conducted across five US agencies over the course of nearly a decade involving hundreds of researchers. One of the primary objectives of the intensive campaign was to investigate the ability of atmospheric inversion techniques to use highly calibrated CO₂ mixing ratio data to estimate CO₂ flux over the major croplands of the United States by comparing the results to an inventory of CO₂ fluxes. Statistics from densely monitored crop production, consisting primarily of corn and soybeans, provided the backbone of a well studied bottom‐up inventory flux estimate that was used to evaluate the atmospheric inversion results. Estimates were compared to the inventory from three different inversion systems, representing spatial scales varying from high resolution mesoscale (PSU), to continental (CSU) and global (CarbonTracker), coupled to different transport models and optimization techniques. The inversion‐based mean CO₂‐C sink estimates were generally slightly larger, 8–20% for PSU, 10–20% for CSU, and 21% for CarbonTracker, but statistically indistinguishable, from the inventory estimate of 135 TgC. While the comparisons show that the MCI region‐wide C sink is robust across inversion system and spatial scale, only the continental and mesoscale inversions were able to reproduce the spatial patterns within the region. In general, the results demonstrate that inversions can recover CO₂ fluxes at sub‐regional scales with a relatively high density of CO₂ observations and adequate information on atmospheric transport in the region.     

High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta

We developed a high-throughput methodology, termed fluorescent tagging of full-length proteins (FTFLP), to analyze expression patterns and subcellular localization of Arabidopsis gene products in planta. Determination of these parameters is a logical first step in functional characterization of the approximately one-third of all known Arabidopsis genes that encode novel proteins of unknown function. Our FTFLP-based approach offers two significant advantages: first, it produces internally-tagged full-length proteins that are likely to exhibit native intracellular localization, and second, it yields information about the tissue specificity of gene expression by the use of native promoters. To demonstrate how FTFLP may be used for characterization of the Arabidopsis proteome, we tagged a series of known proteins with diverse subcellular targeting patterns as well as several proteins with unknown function and unassigned subcellular localization.     

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors—historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short‐wavelength‐sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short‐wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch‐like form that colonized from the Old World 15–20 Ma. During this process, the SWS2 gene accumulated six substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch‐like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected.     

Predicting the Efficacy of Polycyclic Aromatic Hydrocarbon Bioremediation in Creosote-Contaminated Soil Using Bioavailability Assays

Nonexhaustive extraction (propanol, butanol, hydroxypropyl-β-cyclodextrin [HPCD]), persulfate oxidation and biodegradability assays were employed to determine the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in creosote-contaminated soil. After 16 weeks incubation, greater than 89% of three-ring compounds (acenaphthene, anthracene, fluorene, and phenanthrene) and 21% to 79% of four-ring compounds (benz[a]anthracene, chrysene, fluoranthene, and pyrene) were degraded by the indigenous microorganisms under biopile conditions. No significant decrease in five- (benzo[a]pyrene, benzo[b+k]fluoranthene) and six-ring compounds (benz[g,h,i]perylene, indeno[1,2,3-c,d]pyrene) was observed. Desorption of PAHs using propanol or butanol could not predict PAH biodegradability: low-molecular-weight PAH biodegradability was underestimated whereas high-molecular-weight PAH biodegradability was overestimated. Persulfate oxidation and HPCD extraction of creosote-contaminated soil was able to predict three- and four-ring PAH biodegradability; however, the biodegradability of five-ring PAHs was overestimated. These results demonstrate that persulfate oxidation and HPCD extraction are good predictors of PAH biodegradability for compounds with octanol-water partitioning coefficients of < 6.     

Crystal structure of sTALL-1 reveals a virus-like assembly of TNF family ligands

TALL-1/BAFF/BLyS was recently identified as a member of the tumor necrosis factor (TNF) ligand family. The crystal structure of the functional soluble TALL-1 (sTALL-1) has been determined at 3.0 A. sTALL-1 forms a virus-like assembly with 200 A diameter in the crystals, containing 60 sTALL-1 monomers. The cluster formation is mediated by a "flap" region of the sTALL-1 monomer. The virus-like assembly was also detected in solution using gel filtration and electron microscopy. Deletion of the flap region disrupted the formation of the virus-like assembly. The mutant sTALL-1 still bound its receptor but could not activate NF-kappaB and did not stimulate B lymphocyte proliferation. Finally, we found the virus-like cluster of sTALL-1 exists in physiological condition. We propose that this virus-like assembly of sTALL-1 is the functional unit for TALL-1 in vivo.