Coral Reef Disturbance and Recovery Dynamics Differ across Gradients of Localized Stressors in the Mariana Islands

The individual contribution of natural disturbances, localized stressors, and environmental regimes upon longer-term reef dynamics remains poorly resolved for many locales despite its significance for management. This study examined coral reefs in the Commonwealth of the Northern Mariana Islands across a 12-year period that included elevated Crown-of-Thorns Starfish densities (COTS) and tropical storms that were drivers of spatially-inconsistent disturbance and recovery patterns. At the island scale, disturbance impacts were highest on Saipan with reduced fish sizes, grazing urchins, and water quality, despite having a more favorable geological foundation for coral growth compared with Rota. However, individual drivers of reef dynamics were better quantified through site-level investigations that built upon island generalizations. While COTS densities were the strongest predictors of coral decline as expected, interactive terms that included wave exposure and size of the overall fish assemblages improved models (R² and AIC values). Both wave exposure and fish size diminished disturbance impacts and had negative associations with COTS. However, contrasting findings emerged when examining net ecological change across the 12-year period. Wave exposure had a ubiquitous, positive influence upon the net change in favorable benthic substrates (i.e. corals and other heavily calcifying substrates, R² = 0.17 for all reeftypes grouped), yet including interactive terms for herbivore size and grazing urchin densities, as well as stratifying by major reeftypes, substantially improved models (R² = 0.21 to 0.89, lower AIC scores). Net changes in coral assemblages (i.e., coral ordination scores) were more sensitive to herbivore size or the water quality proxy acting independently (R² = 0.28 to 0.44). We conclude that COTS densities were the strongest drivers of coral decline, however, net ecological change was most influenced by localized stressors, especially herbivore sizes and grazing urchin densities. Interestingly, fish size, rather than biomass, was consistently a better predictor, supporting allometric, size-and-function relationships of fish assemblages. Management implications are discussed.     

Climate‐change refugia in the sheltered bays of Palau: analogs of future reefs

Coral bleaching and mortality are predicted to increase as climate change‐induced thermal‐stress events become more frequent. Although many studies document coral bleaching and mortality patterns, few studies have examined deviations from the expected positive relationships among thermal stress, coral bleaching, and coral mortality. This study examined the response of >30,000 coral colonies at 80 sites in Palau, during a regional thermal‐stress event in 2010. We sought to determine the spatial and taxonomic nature of bleaching and examine whether any habitats were comparatively resistant to thermal stress. Bleaching was most severe in the northwestern lagoon, in accordance with satellite‐derived maximum temperatures and anomalous temperatures above the long‐term averages. Pocillopora populations suffered the most extensive bleaching and the highest mortality. However, in the bays where temperatures were higher than elsewhere, bleaching and mortality were low. The coral‐community composition, constant exposure to high temperatures, and high vertical attenuation of light caused by naturally high suspended particulate matter buffered the corals in bays from the 2010 regional thermal‐stress event. Yet, nearshore reefs are also most vulnerable to land‐use change. Therefore, nearshore reefs should be given high conservation status because they provide refugia for coral populations as the oceans continue to warm.     

Ab initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate

Abstract

Snitric oxide plays important roles in protein S-nitrosylation, in which thionitroxide (RSNHO) may serve as a signal at the cysteine site. Car-Parrinello metadynamics method was employed to investigate the possible fate of thionitroxide (S-nitroxide) in S-nitrosylation, focusing on S–N decomposition that leads to HNO, NO and even thiyl radical. As a result, the lowest-energy pathway from thiol towards S-nitrosothiol via thionitroxide was predicted to be feasible in a form of RSH + 2 NO? = RSNO + HNO. This equilibrium for the chemical modification was likely controlled by surrounding environment, that is, by aqueous solution and methanol in this simulation, and probably by dynamic structure of polar residues in S-nitrosylated protein. This work implied that the general importance of the temporal and spatial transformation of allosteric effect in a predictive modelling of protein post-translational modification could be briefly attested with the artificially intelligent CPMD algorithm.     

The measurement of actin concentration in solution: a comparison of methods

Intrinsic optical density, Folin, and Biuret color development have been carefully studied as methods of determining actin concentration in solution. It appears that the Lowry (Folin) method is the most sensitive and reliable method as standardized by Kjeldahl analysis. Intrinsic optical density is also found to be a reliable method and the extinction coefficients of F and G actin at 280 and 290 nm are determined. The Biuret reaction is found to be the least reliable of the three methods for determining the concentration of actin in solution.     

Tempo and mode of concerted evolution in the L1 repeat family of mice

A 300-bp DNA sequence has been determined for 30 (10 from each of three species of mice) random isolates of a subset of the long interspersed repeat family L1. From these data we conclude that members of the L1 family are evolving in concert at the DNA sequence level in Mus domesticus, Mus caroli, and Mus platythrix. The mechanism responsible for this phenomenon may be either duplicative transposition, gene conversion, or a combination of the two. The amount of intraspecies divergence averages 4.4%, although between species base substitutions accumulate at the rate of approximately 0.85%/Myr to a maximum divergence of 9.1% between M. platythrix and both M. domesticus and M. caroli. Parsimony analysis reveals that the M. platythrix L1 family has evolved into a distinct clade in the 10-12 Myr since M. platythrix last shared a common ancestor with M. domesticus and M. caroli. The parsimony tree also provides a means to derive the average half-life of L1 sequences in the genome. The rates of gain and loss of individual copies of L1 were estimated to be approximately equal, such that approximately one-half of them turn over every 3.3 Myr.      

Agents of the mind

The higher order circuitry of the brain is comprised of a large-scale network of cerebral cortical areas that are individually regulated by loops through subcortical structures, particularly through the basal ganglia and cerebellum. These subcortical loops have powerful computational architectures. Using, as an example, the relatively well-understood processing that occurs in the cortical/basal ganglionic/cerebellar distributed processing module that generates voluntary motor commands, I postulate that a network of analogous agents is an appropriate framework for exploring the dynamics of the mind.     

Induction of prophage lambda by chlorinated pesticides

Chlorinated organics represent an important class of environmental carcinogens. However, only a small percentage of the carcinogens of this chemical class are genotoxic in prokaryotic bioassays such as the Salmonella assay. In an effort to identify a short-term assay sensitive to chlorinated carcinogens, we have tested a group of chlorinated pesticides, most of which are carcinogenic in rodents, in a prophage-induction assay developed by Rossman et al. (1984). The Microscreen phage-induction assay is a rapid, inexpensive, miniaturized system that uses the induction of prophage lambda in Escherichia coli as an indicator of genetic damage. It has been used successfully to screen complex environmental samples for genotoxicants and has detected carcinogenic metals that are refractory in the Salmonella assay. The pesticides tested were malathion, monuron, p,p'-DDT, mirex, lindane, nitrofen, chlordane, toxaphene, captan, and dichlorvos. All but the first 4 induced prophage. The remaining pesticides were ranked as follows according to induction potency in the presence of S9: captan greater than dichlorvos greater than toxaphene greater than lindane greater than nitrofen greater than chlordane. Rankings were similar in the absence of S9. Of these 6 pesticides, only nitrofen required S9 to induce prophage. Comparisons with mutagenesis data in Salmonella indicated that the Microscreen assay detected as genotoxic each of the pesticides that were mutagenic in Salmonella; moreover, it detected 2 additional carcinogens (chlordane and lindane) that were not mutagenic in the Salmonella assay. The possible use of the Microscreen phage-induction assay to detect chlorinated organics is discussed.     

Speciation of trace elements in proteins in human and bovine serum by size exclusion chromatography and inductively coupled plasma-mass spectrometry with a magnetic sector mass spectrometer

 Proteins are separated by size exclusion chromatography while atomic ions from the inorganic elements are detected on-line by inductively coupled plasma-mass spectrometry. A double focusing mass analyzer provides very high sensitivity, low background, and sufficient spectral resolution to separate the atomic ions of interest from most polyatomic ions at the same nominal m/z value. The chromatograms show the distribution of the elements of interest between protein-bound and free fractions and provide the approximate molecular weights of those protein fractions that contain the elements monitored. The distribution of various elements, including V, Mo, Fe, Co, Mn, and lanthanides, in human or bovine serum samples are shown. Alkali metals and Tl are present primarily as free metal ions and are not bound to proteins. Inorganic elements spiked into the serum samples can be followed into various proteins. EDTA does not remove Fe, Pb, Sn, or Th from the proteins but does extract Mn from some proteins. Procedures for determining the effects of breaking disulfide linkages on the metal binding characteristics of proteins are also described. Received: 22 March 1999 / Accepted: 16 June 1999     

Bronchial epithelial cells are rendered insensitive to glucocorticoid transactivation by transforming growth factor-β1

Background

We have previously shown that transforming growth factor-beta (TGF-beta) impairs glucocorticoid (GC) function in pulmonary epithelial cell-lines. However, the signalling cascade leading to this impairment is unknown. In the present study, we provide the first evidence that TGF-beta impairs GC action in differentiated primary air-liquid interface (ALI) human bronchial epithelial cells (HBECs). Using the BEAS-2B bronchial epithelial cell line, we also present a systematic examination of the known pathways activated by TGF-beta, in order to ascertain the molecular mechanism through which TGF-beta impairs epithelial GC action.

Methods

GC transactivation was measured using a Glucocorticoid Response Element (GRE)–Secreted embryonic alkaline phosphatase (SEAP) reporter and measuring GC-inducible gene expression by qRT-PCR. GC transrepression was measured by examining GC regulation of pro-inflammatory mediators. TGF-beta signalling pathways were investigated using siRNA and small molecule kinase inhibitors. GRα level, phosphorylation and sub-cellular localisation were determined by western blotting, immunocytochemistry and localisation of GRα–Yellow Fluorescent Protein (YFP). Data are presented as the mean ± SEM for n independent experiments in cell lines, or for experiments on primary HBEC cells from n individual donors. All data were statistically analysed using GraphPad Prism 5.0 (Graphpad, San Diego, CA). In most cases, two-way analyses of variance (ANOVA) with Bonferroni post-hoc tests were used to analyse the data. In all cases, P <0.05 was considered to be statistically significant.

Results

TGF-beta impaired Glucocorticoid Response Element (GRE) activation and the GC induction of several anti-inflammatory genes, but did not broadly impair the regulation of pro-inflammatory gene expression in A549 and BEAS-2B cell lines. TGF-beta-impairment of GC transactivation was also observed in differentiated primary HBECs. The TGF-beta receptor (ALK5) inhibitor SB431541 fully prevented the GC transactivation impairment in the BEAS-2B cell line. However, neither inhibitors of the known downstream non-canonical signalling pathways, nor knocking down Smad4 by siRNA prevented the TGF-beta impairment of GC activity.

Conclusions

Our results indicate that TGF-beta profoundly impairs GC transactivation in bronchial epithelial cells through activating ALK5, but not through known non-canonical pathways, nor through Smad4-dependent signalling, suggesting that TGF-beta may impair GC action through a novel non-canonical signalling mechanism.     

Free radical biology and medicine: it's a gas, man!

We review gases that can affect oxidative stress and that themselves may be radicals. We discuss O(2) toxicity, invoking superoxide, hydrogen peroxide, and the hydroxyl radical. We also discuss superoxide dismutase (SOD) and both ground-state, triplet oxygen ((3)O(2)), and the more energetic, reactive singlet oxygen ((1)O(2)). Nitric oxide ((*)NO) is a free radical with cell signaling functions. Besides its role as a vasorelaxant, (*)NO and related species have other functions. Other endogenously produced gases include carbon monoxide (CO), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S). Like (*)NO, these species impact free radical biochemistry. The coordinated regulation of these species suggests that they all are used in cell signaling. Nitric oxide, nitrogen dioxide, and the carbonate radical (CO(3)(*-)) react selectively at moderate rates with nonradicals, but react fast with a second radical. These reactions establish "cross talk" between reactive oxygen (ROS) and reactive nitrogen species (RNS). Some of these species can react to produce nitrated proteins and nitrolipids. It has been suggested that ozone is formed in vivo. However, the biomarkers that were used to probe for ozone reactions may be formed by non-ozone-dependent reactions. We discuss this fascinating problem in the section on ozone. Very low levels of ROS or RNS may be mitogenic, but very high levels cause an oxidative stress that can result in growth arrest (transient or permanent), apoptosis, or necrosis. Between these extremes, many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive. Such adaptive mechanisms are thought to be of evolutionary importance.