A mathematical framework for inferring connectivity in probabilistic neuronal networks

We describe an approach for determining causal connections among nodes of a probabilistic network even when many nodes remain unobservable. The unobservable nodes introduce ambiguity into the estimate of the causal structure. However, in some experimental contexts, such as those commonly used in neuroscience, this ambiguity is present even without unobservable nodes. The analysis is presented in terms of a point process model of a neuronal network, though the approach can be generalized to other contexts. The analysis depends on the existence of a model that captures the relationship between nodal activity and a set of measurable external variables. The mathematical framework is sufficiently general to allow a large class of such models. The results are modestly robust to deviations from model assumptions, though additional validation methods are needed to assess the success of the results.     

Age-dependent requirement of AKAP150-anchored PKA and GluR2-lacking AMPA receptors in LTP

Association of PKA with the AMPA receptor GluR1 subunit via the A kinase anchor protein AKAP150 is crucial for GluR1 phosphorylation. Mutating the AKAP150 gene to specifically prevent PKA binding reduced PKA within postsynaptic densities (>70%). It abolished hippocampal LTP in 7-12 but not 4-week-old mice. Inhibitors of PKA and of GluR2-lacking AMPA receptors blocked single tetanus LTP in hippocampal slices of 8 but not 4-week-old WT mice. Inhibitors of GluR2-lacking AMPA receptors also prevented LTP in 2 but not 3-week-old mice. Other studies demonstrate that GluR1 homomeric AMPA receptors are the main GluR2-lacking AMPA receptors in adult hippocampus and require PKA for their functional postsynaptic expression during potentiation. AKAP150-anchored PKA might thus critically contribute to LTP in adult hippocampus in part by phosphorylating GluR1 to foster postsynaptic accumulation of homomeric GluR1 AMPA receptors during initial LTP in 8-week-old mice.     

Pigment analysis of "Candidatus Chlorothrix halophila," a green filamentous anoxygenic phototrophic bacterium

The pigment composition of "Candidatus Chlorothrix halophila," a filamentous anoxygenic phototrophic bacterium found in Baja California Sur, Mexico, was determined. Previous work showed that bacteriochlorophyll c (BChl c) was the major pigment in "Ca. Chlorothrix halophila," but it was not clear if this bacterium also contains BChl a (J. A. Klappenbach and B. K. Pierson, Arch. Microbiol. 181:17-25, 2004). Here we show that in addition to BChl c, a small amount of a pigment that is spectrally indistinguishable from BChl a is present in cell extracts of "Ca. Chlorothrix halophila." Nevertheless, the BChl a-like pigment from "Ca. Chlorothrix halophila" has a different molecular weight and a different high-performance liquid chromatography elution time than BChl a from other photosynthetic bacteria. Based on mass spectrometry and other spectroscopic analysis, we determined that the BChl a-like pigment in "Ca. Chlorothrix halophila" contains a tetrahydrogeranylgeraniol tail rather than the phytol tail that is present in BChl a. The carotenoids and major BChl c homologs in "Ca. Chlorothrix halophila" were also identified. BChls c were found to be farnesol esterified and geranylgeraniol esterified.     

Tumor necrosis factor-alpha reduces argininosuccinate synthase expression and nitric oxide production in aortic endothelial cells

Endothelial dysfunction associated with elevated serum levels of TNF-alpha observed in diabetes, obesity, and congenital heart disease results, in part, from the impaired production of endothelial nitric oxide (NO). Cellular NO production depends absolutely on the availability of arginine, substrate of endothelial nitric oxide synthase (eNOS). In this report, evidence is provided demonstrating that treatment with TNF-alpha (10 ng/ml) suppresses not only eNOS expression but also the availability of arginine via the coordinate suppression of argininosuccinate synthase (AS) expression in aortic endothelial cells. Western blot and real-time RT-PCR demonstrated a significant and dose-dependent reduction of AS protein and mRNA when treated with TNF-alpha with a corresponding decrease in NO production. Reporter gene analysis demonstrated that TNF-alpha suppresses the AS proximal promoter, and EMSA analysis showed reduced binding to three essential Sp1 elements. Inhibitor studies suggested that the repression of AS expression by TNF-alpha may be mediated, in part, via the NF-kappaB signaling pathway. These findings demonstrate that TNF-alpha coordinately downregulates eNOS and AS expression, resulting in a severely impaired citrulline-NO cycle. The downregulation of AS by TNF-alpha is an added insult to endothelial function because of its important role in NO production and in endothelial viability.     

Bradykinin B1 antagonists: biphenyl SAR studies in the cyclopropanecarboxamide series

SAR study of the biphenyl region of cyclopropanecarboxamide derived bradykinin B(1) antagonists was examined. Incorporation of a pyridine in place of the proximal phenyl ring and chlorination of the distal phenyl ring proved to be well tolerated and provided compounds with improved pharmacokinetic profiles, CNS penetration, and enhanced receptor occupancy.     

Endothelial nitric oxide production is tightly coupled to the citrulline–NO cycle

Nitric oxide (NO) is an important vasorelaxant produced along with L-citrulline from L-arginine in a reaction catalyzed by endothelial nitric oxide synthase (eNOS). Previous studies suggested that the recycling of L-citrulline to L-arginine is essential for NO production in endothelial cells. However, there is no direct evidence demonstrating the degree to which the recycling of L-citrulline to L-arginine is coupled to NO production. We hypothesized that the amount of NO formed would be significantly higher than the amount of L-citrulline formed due to the efficiency of L-citrulline recycling via the citrulline-NO cycle. To test this hypothesis, endothelial cells were incubated with [14C]-L-arginine and stimulated by various agents to produce NO. The extent of NO and [14C]-L-citrulline formation were simultaneously determined. NO production exceeded apparent L-citrulline formation of the order of 8 to 1, under both basal and stimulated conditions. As further support, alpha-methyl-DL-aspartate, an inhibitor of argininosuccinate synthase (AS), a component of the citrulline-NO cycle, inhibited NO production in a dose-dependent manner. The results of this study provide evidence for the essential and efficient coupling of L-citrulline recycling, via the citrulline-NO cycle, to endothelial NO production.     

Soil Organic Phosphorus Transformations During Pedogenesis

Abstract Long-term changes in soil phosphorus influence ecosystem development and lead to a decline in the productivity of forests in undisturbed landscapes. Much of the soil phosphorus occurs in a series of organic compounds that differ in their availability to organisms, but changes in the relative abundance of these compounds during pedogenesis remain unknown. We used alkaline extraction and solution phosphorus-31 nuclear magnetic resonance spectroscopy to assess the chemical nature of soil organic phosphorus along a 120,000-year post-glacial chronosequence at Franz Josef, New Zealand. Inositol phosphates, DNA, phospholipids, and phosphonates accumulated rapidly during the first 500 years of soil development characterized by nitrogen limitation of biological productivity, but then declined slowly to low concentrations in older soils characterized by intense phosphorus limitation. However, the relative contribution of the various compounds to the total organic phosphorus varied along the sequence in dramatic and surprising ways. The proportion of inositol hexakisphosphate, conventionally considered to be relatively recalcitrant in the environment, declined markedly in older soils, apparently due to a corresponding decline in amorphous metal oxides, which weather to crystalline forms during pedogenesis. In contrast, the proportion of DNA, considered relatively bioavailable in soil, increased continually throughout the sequence, due apparently to incorporation within organic structures that provide protection from biological attack. The changes in soil organic phosphorus coincided with marked shifts in plant and microbial communities, suggesting that differences in the forms and bioavailability of soil organic phosphorus have ecological significance. Overall, the results strengthen our understanding of phosphorus transformations during pedogenesis and provide important insight into factors regulating the composition of soil organic phosphorus.     

Learning from clinical medicine to improve the use of surrogates in ecology

Surrogates are used widely in ecology to detect or monitor changes in the environment that are too difficult or costly to assess directly. Yet most work on surrogates to date has been correlative, with little work on their predictive capacity or the circumstances under which they work. Our suggestion is to revisit and learn from research in the clinical medical sciences, including the causal statistical frameworks available to validate relationships between treatments, surrogate variables, and the outcome of interest. We adapt this medical thinking to ecology by providing a new framework that involves specification of the surrogate model, statistical validation, and subsequent evaluation in a range of spatial and temporal contexts. An inter‐disciplinary surrogate concept will allow for a more rigorous approach to validating and evaluating proxy variables, thus advancing the selection and application of surrogates in ecology. Synthesis We draw together ideas from the medical sciences to define an explicit surrogate concept that has not previously been used in ecology. We present a new framework for specifying surrogate models involving validation using a causal framework, and subsequent re‐evaluation in different spatial and temporal contexts – an approach closely aligned with that used by researchers in the clinical medical sciences. This rigorous method can advance the science underpinning the application of surrogates in ecology by shifting the focus away from correlative understanding to one that focuses instead on causation and prediction. An improved use of surrogates is imperative if we are to meet the challenge of properly measuring and understanding the multifarious and complex problems in contemporary ecology.