Biogeochemical Implications of Episodic Impoundment in a Restored Tidal Marsh of San Francisco Bay,California

Impounded tidal conditions often compromise coastal marsh restoration goals, through vegetation loss and other biogeochemical feedbacks. To determine if episodic marsh impoundments could be partially responsible for the observed cordgrass (Spartina foliosa) dieback at Crissy Field, Golden Gate National Recreation Area, we examined sulfur chemistry and plant stress along transects between and during tidal inlet closure events from 2007 to 2008. During closures, porewater sulfide (PW S^2?) concentrations did not respond consistently among sites, nor did they increase to levels likely to cause stress damage to cordgrass (>1 mM). However, sediment solid‐phase total reduced sulfur (TRS) concentrations did respond strongly to closures both at surface and subsurface depth intervals, and they were greatest in sites with high organic matter content (>5%). The temporal patterns of both PW S^2? and TRS suggest that while sulfate reduction may be enhanced during closure events, the free sulfide produced is largely precipitated into solid‐phase minerals. Even without millimolar levels of PW S^2?, plant stress was observed during closures, as indicated by a buildup of ethanol in root tissues, a by‐product of fermentative respiration brought on by limited oxygen availability. Further, enhanced sulfate reduction may be related to the higher relative concentrations of methylmercury in low intertidal surface sediments observed during closure events. These data suggest that, in support of vegetated tidal marsh restoration goals, tidal flows should be maintained actively to reduce the impact of impoundment events on marsh biogeochemistry and productivity.     

Multispectral optoacoustic tomography of muscle perfusion and oxygenation under arterial and venous occlusion: A human pilot study

Perfusion and oxygenation are critical parameters of muscle metabolism in health and disease. They have been both the target of many studies, in particular using near‐infrared spectroscopy (NIRS). However, difficulties with quantifying NIRS signals have limited a wide dissemination of the method to the clinics. Our aim was to investigate whether clinical multispectral optoacoustic tomography (MSOT) could enable the label‐free imaging of muscle perfusion and oxygenation under clinically relevant challenges: the arterial and venous occlusion. We employed a hybrid clinical MSOT/ultrasound system equipped with a hand‐held scanning probe to visualize hemodynamic and oxygenation changes in skeletal muscle under arterial and venous occlusions. Four (N = 4) healthy volunteers were scanned over the forearm for both 3‐minute occlusion challenges. MSOT‐recorded pathophysiologically expected results during tests of disturbed blood flow with high resolution and without the need for contrast agents. During arterial occlusion, MSOT‐extracted Hb‐values showed an increase, while HbO₂‐ and total blood volume (TBV)‐values remained roughly steady, followed by a discrete increase during the hyperemic period after cuff deflation. During venous occlusion, results showed a clear increase in intramuscular HbO₂, Hb and TBV within the segmented muscle area. MSOT was found to be capable of label‐free non‐invasive imaging of muscle hemodynamics and oxygenation under arterial and venous occlusion. We introduce herein MSOT as a novel modality for the assessment of vascular disorders characterized by disturbed blood flow, such as acute limb ischemia and venous thrombosis.     

Systems Biology: The elements and principles of Life

Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam’s razor and minimum energy/maximal efficiency. By referring to biochemical experiments on control and regulation, and on flux balancing in yeast, we show that these paradigms are inapt. Systems Biology does not quite converge with biology either: Although it certainly requires accurate ‘stamp collecting’, it discovers quantitative laws. Systems Biology is a science of its own, discovering own fundamental principles, some of which we identify here.     

Purification and properties of the antizymes of Escherichia coli to ornithine decarboxylase

The purification of the antizymes to ornithine decarboxylase of Escherichia coli to homogeneity is detailed. An acidic component, pI 3.8, and two basic histone-like proteins, pI above 9.5, are described. The two latter proteins constitute approximately 90% of the total antizyme activity.     

Coralligène formations in the eastern Mediterranean Sea: Morphology, distribution, mapping and relation to fisheries in the southern Aegean Sea (Greece) based on high-resolution acoustics

Coralline algae are one of the most important constructors of biogenic habitats. In the Mediterranean Sea, the dominant coralline algae species form crusts comprising formations known as coralligène, considered as very important fishing grounds by fishermen. Due to the destructive effect of fishing gear activities over coralligène, these formations were recently protected from the use of active benthic gears by the EU 1967/2006 Mediterranean fisheries management Regulation. However, the lack of maps and information on their distribution makes the effective application of these measures impossible. The present publication contributes to the mapping of coralligène in the southern Aegean Sea (eastern Mediterranean), and to the study of coralline algae formation morphology, distribution, development conditions and relation to fisheries using a combination of single-beam echo sounder, sidescan sonar, sub-bottom profiler recordings and biological and sedimentological ground-truthing techniques. The coralligène formations were recognized as two distinct acoustic signatures of localized backscatter facies distinguishable from other hard substrate reflectors at depths ranging from 55.9 to 114.0 m, but mainly between 70 and 90 m. Two types of formations were identified: minute reefs 0.5-2.5 m in height and superficial layer formations no more than 0.2 m thick over the substrate. The seismic profiles revealed a cavernous internal structure of the minute reefs and recorded their development on both hard and soft substrates. The distribution of formations was contagious, creating aggregations. The finding of superficial layer formations and coralline shreds around minute coralligène reefs indicated that the former could be an intermediate development type between isolated small coralline pebbles, rhodoliths, and minute reefs. Regarding the development conditions, sidescan sonar imagery indicated that the optimal conditions for the establishment and development of coralligène formations are medium intensity currents. Concerning human activity over coralligène, trawl traces were recorded near but not over minute reefs and both near and crossing superficial layer type aggregations, while a submarine cable was also recorded among minute reefs. The mapping of coralligène aggregation areas is essential for the application of the EU Regulation and the protection of this important marine habitat.     

Quantitative relationships between boron and mannitol concentrations in phloem exudates of Olea europaea leaves under contrasting boron supply conditions

Root exudates are implicated in the chemical defense of plants, but testing such hypotheses has been hindered by the difficulties of quantifying allelochemical concentrations in soil. Here we describe a new, simple method to quantify the dynamics of non-polar root exudates in soil. Novel soil probes were constructed using stainless steel wire inserted into polydimethylsiloxane (PDMS) tubing. Probes were inserted into soil for 24 h, removed and extracted, and analyzed by HPLC. Lipophilic thiophenes produced by roots of Tagetes and Rudbeckia species were chosen as candidate compounds to test the method. Probes recovered microgram quantities of the highly phytotoxic thiophenes 5-(3-buten-1-ynyl)-2,2′-bithienyl (BBT) and α-terthienyl per probe per day from the root zone of Tagetes patula, and distribution of thiophenes beneath plants was spatially and temporally heterogeneous. Flux-proportional sampling of soil provides a means to test hypotheses about the role of root exudates in plant–plant and other interactions.     

Conformational requirements for molecular recognition of acetylcholine receptor main immunogenic region (MIR) analogues by monoclonal anti-MIR antibody: A two-dimensional nuclear magnetic resonance and molecular dynamics approach

The conformational properties of two [D -A⁷⁰, A⁷⁶] and [Aib⁷⁰, A⁷⁶] analogues of the α67–76 Torpedo acetylcholine receptor fragment, with low binding capacity for the anti main immunogenic region (MIR) antibodies, were studied in DMSO by two-dimensional nmr techniques and molecular dynamics simulations. The results were compared to the free and bound conformations of the [A⁷⁶] analogue, which has twice more affinity for the anti-MIR monoclonal antibody 6 (mAb6), than the natural Torpedo sequence. It appeared that a single substitution of the A⁷⁰, at a crucial position, by the D -A⁷⁰ or Aib⁷⁰, could modify completely the conformational behavior of the peptide and reduced its recognition by the anti-MIR antibody. The WNPADY rigid structure at the N-terminal part was essential for antibody recognition. The adjacent more flexible C-terminal sequence (GGIK) gives additional stability to the monoclonal antibody–peptide complex probably due to an adequate orientation of the peptide side chains in the complex, by setting them in close contact with the antibody. © 1993 John Wiley & Sons, Inc.     

Application of the fourth universal definition of myocardial infarction in clinical practice

Abstract

Purpose: The Fourth Universal Definition of Myocardial Infarction (MI) has highlighted the different pathophysiological mechanisms that may lead to ischaemic and non-ischaemic myocardial injury and has emphasised that the diagnosis of myocardial infarction requires the presence of acute myocardial ischaemia in the setting of acute myocardial injury. This case based review intends to illustrate basic principles on how to apply this new, revised definition in clinical practice.

Methods and Results: The distinction between different types of MIs (type 1 or type 2) and the delineation of MI from acute non-ischaemic myocardial injury may be challenging in individual patients, which is illustrated by presenting and discussing real-life routine cases.

Conclusions: Type 1?MI is a consequence of coronary plaque rupture or erosion with intracoronary thrombus formation that is usually apparent on coronary angiography. Plausible triggering mechanisms causing myocardial oxygen supply/demand mismatch must be identified for the diagnosis of type 2?MI and its treatment should focus initially on management of the underlying disease attributable to acute myocardial ischaemia.     

Species co-occurrence: the case of congeneric species and a causal approach to patterns of species association

Aim To test whether congeneric species are significantly associated with one another in space, either positively or negatively. Also, to provide a framework for a causal investigation of co‐occurrence patterns by a parallel comparison of interactions in geographical and ecological data matrices. Location For the analysis of congeneric species’ co‐occurrences we used 30 matrices covering a wide range of taxa and geographical areas, while for the causal investigation we used the distribution of 50 terrestrial isopod species on 20 islands and 264 sampling stations in the central Aegean archipelago, as well as a number of ecological variables for each sampling station. Methods We developed a software program (cooc ) that incorporates the species‐by‐species approach to co‐occurrence analysis using EcoSim's output of prior null model analysis of co‐occurrence. We describe this program in detail, and use it to investigate one of the most common assembly rules, namely, the decreased levels of co‐occurrence among congeneric species pairs. For the causal analysis, we proceed likewise, cross‐checking the results from the geographical and the ecological matrices. There is only one possible combination of results that can support claims for direct competition among species. Results We do not get any strong evidence for widespread competition among congeneric species, while most communities investigated do not show significant patterns of species associations. The causal analysis suggests that the principal factors behind terrestrial isopod species associations are of historical nature. Some exceptional cases are also discussed. Main conclusions Presence/absence data for a variety of taxa do not support the assembly rule that congeneric species are under more intense competition compared to less related species. Also, these same data do not suggest strong interactions among species pairs, regardless of taxonomic status. When significant species associations can be seen in such matrices, they mainly reflect the effects of history or of habitat requirements.     

Between-island compositional dissimilarity of avian communities

Compositional dissimilarity patterns of biotic communities can vary among different types of insular systems and among taxa with different dispersal abilities. In this work we examined compositional dissimilarity patterns of four avian groups, namely birds of prey, waterbirds, seabirds and landbirds, in various insular systems around the world. Compositional dissimilarity of avian communities was calculated for 25 presence-absence matrices compiled from the literature. We used generalized linear mixed-effects models to check for differences in between-island compositional dissimilarity among the aforementioned avian groups that differ in their dispersal abilities, as well as between two different types of insular systems, oceanic and continental shelf. In agreement with our original hypothesis, landbirds which have relatively poorer dispersal abilities than birds of prey and waterbirds, exhibit higher between-island compositional dissimilarity compared to these two avian groups. On the contrary, seabirds present a deviation from the expected pattern, since they show higher between-island compositional dissimilarity compared to landbirds, even though they also have better dispersal abilities than landbirds, which can be explained by the relatively irregular occurrence of proper breeding habitats among islands for this avian group. Island type (oceanic or continental shelf) does not appear to affect between-island compositional dissimilarity of avian communities. Distance, area and elevation differences among islands are positively related to compositional dissimilarity. In conclusion, compositional dissimilarity of avian communities differs between avian groups but cannot always be associated with differences in the dispersal ability among these groups.