Restoration of marine ecosystems: Understanding possible futures for optimal outcomes

Accelerating declines in the extent, quality and functioning of the world's marine ecosystems have generated an upsurge in focus on practical solutions, with ecosystem restoration becoming an increasingly attractive mitigation strategy for systems as diverse as coral reefs, mangroves and tidal flats. While restoration is popular because it promises positive outcomes and a return to something approaching unimpacted condition and functioning, it involves substantial public and private investment, both for the initial restoration activity and for on-going maintenance of the restored asset. This investment often affords one big chance to get things right before irretrievable damage is done. As a result, precise, well considered and accountable decision-making is needed to determine the specific focus for restoration, the scale of restoration, the location for deploying restoration activities, and indeed whether or not restoration is necessary or even possible. We explore the environmental/ecological considerations and constraints governing optimal decisions about the nature, location and prioritisation of restoration activities in marine ecosystems, and in particular the constraints on achieving understanding of possible futures and the likelihood of achieving them. We conclude that action must be informed by a context-specific understanding of the historical situation, the current situation, the constraints on change, the range of potential outcome scenarios, and the potential futures envisioned.

Stakeholder engagement in the governance of marine migratory species: barriers and building blocks

Meaningful stakeholder engagement is important to collaborative decision-making and to effective polycentric governance, particularly when managing cross-scale environmental issues like those involving marine migratory species. In this paper, we explore the barriers to, and opportunities for, stakeholder involvement in the governance of threats to marine migratory species in eastern Australia, using semi-structured qualitative interviews and a focus group, as an example of the generic problem of managing migratory species within a large range state with multiple jurisdictions. Respondents identified several barriers to, and opportunities for, improved stakeholder involvement in the governance of marine migratory species, corresponding to 4 main themes: decision-making processes, information sharing, institutional structures, and participation processes. Respondents indicated that the governance system protecting marine turtles, dugongs, humpback whales, and non-threatened migratory shorebirds in eastern Australia would benefit from the introduction of new information pathways, reformed institutional structures (including environmental legislation), and improved participatory pathways for non-government stakeholders. Such changes could help harmonise the process of managing these species, leading to more effective conservation management throughout their range.

Comparison of penetrating and non-penetrating captive bolt in an alternative occipital approach in calves

The objective of this study was to describe the effect of penetrating or non-penetrating captive bolt using an occipital approach in 4–5 month old, Holstein steers weighing between 100–200 kg. Twelve calves were divided into two treatment groups; penetrating captive bolt (PCB; n = 6) and non-penetrating captive bolt (NPCB; n = 6). This sample size was chosen out of convenience and in conjunction with a separate study. Each calf was sedated with xylazine hydrochloride, then a captive-bolt device, outfitted with a standard penetrating bolt or a non-penetrating bolt, was placed flush on the dorsal midline of the cranium at the external occipital protuberance and aimed downward as though to intersect the intermandibular area. Following impact, indicators for loss of consciousness, such as respiration, righting response, corneal reflex, movement and vocalisation were recorded and characterised along with electrocardiogram and electroencephalogram recordings. After a 5-min observation period, all calves were administered potassium chloride. All calves experienced immediate and sustained loss of consciousness. The mean (± SEM) time to cessation of respiration was 60 (± 53.67) and 0 (± 0.0) s for PCB and NPCB, respectively. The mean time to cessation of convulsions was 310.4 (± 79.74) and 180.0 (± 60.24) s, respectively, and the mean number of convulsions was 2.75 (± 1.03) and 2.0 (± 0.837) for PCB and NPCB, respectively. Isoelectric EEG patterns were observed in 3/5 PCB and 3/4 NPCB with mean time to onset of isoelectric pattern in 69.0(± 52.24) and 113.5 (± 56.87) s. Both treatments induced a successful stun, which suggests these techniques are appropriate for humane euthanasia in calves of this age.

Our Environmental Value Orientations Influence How We Respond to Climate Change

People variably respond to global change in their beliefs, behaviors, and grief (associated with losses incurred). People that are less likely to believe in climate change, adopt pro-environmental behaviors, or report ecological grief are assumed to have different psycho-cultural orientations, and do not perceive changes in environmental condition or any impact upon themselves. We test these assumptions within the context of the Great Barrier Reef (GBR), a region currently experiencing significant climate change impacts in the form of coral reef bleaching and increasingly severe cyclones. We develop knowledge of environmental cultural services with the Environmental Schwartz Value Survey (ESVS) into four human value orientations that can explain individuals’ environmental beliefs and behaviors: biospheric (i.e., concern for environment), altruistic (i.e., concern for others, and intrinsic values), egoistic (i.e., concern for personal resources) and hedonic values (i.e., concern for pleasure, comfort, esthetic, and spirituality). Using face-to-face quantitative survey techniques, where 1,934 residents were asked to agree or disagree with a range of statements on a scale of 1–10, we investigate people’s (i) environmental values and value orientations, (ii) perceptions of environmental condition, and (iii) perceptions of impact on self. We show how they relate to the following climate change responses; (i) beliefs at a global and local scale, (ii) participation in pro-environmental behaviors, and (iii) levels of grief associated with ecological change, as measured by respective single survey questions. Results suggest that biospheric and altruistic values influenced all climate change responses. Egoistic values were only influential on grief responses. Perception of environmental change was important in influencing beliefs and grief, and perceptions of impact on self were only important in influencing beliefs. These results suggest that environmental managers could use people’s environmental value orientations to more effectively influence climate change responses toward environmental stewardship and sustainability. Communications that target or encourage altruism (through understanding and empathy), biospherism (through information on climate change impacts on the environment), and egoism (through emphasizing the benefits, health and wellbeing derived from a natural resource in good condition), could work.

Multifocal multiphoton excitation and time correlated single photon counting detection for 3-D fluorescence lifetime imaging

We report a multifocal multiphoton time-correlated single photon counting (TCSPC) fluorescence lifetime imaging (FLIM) microscope system that uses a 16 channel multi-anode PMT detector. Multiphoton excitation minimizes out-of-focus photobleaching, multifocal excitation reduces non-linear in-plane photobleaching effects and TCSPC electronics provide photon-efficient detection of the fluorescence decay profile. TCSPC detection is less prone to bleaching- and movement-induced artefacts compared to wide-field time-gated or frequency-domain FLIM. This microscope is therefore capable of acquiring 3-D FLIM images at significantly increased speeds compared to single beam multiphoton microscopy and we demonstrate this with live cells expressing a GFP tagged protein. We also apply this system to time-lapse FLIM of NAD(P)H autofluorescence in single live cells and report measurements on the change in the fluorescence decay profile following the application of a known metabolic inhibitor.

From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics

Eukaryotic genomes are functionally compartmentalized into chromatin domains by their attachment to a supporting structure that has traditionally been termed the nuclear matrix. Present evidence indicates the dynamics of this entity, which requires particular properties of the elements that mediate this kind of interaction. Above all, this is enabled by the so-called 'mass binding phenomenon' by which scaffold/matrix-attachment regions (S/MARs) reversibly associate with ubiquitous factors. Recent investigations and novel techniques have shown that these contacts can be altered by modulators as well as by specific interactions with the components of enhancers and locus control regions.

Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains

Recent evidence adds support to a traditional concept according to which the eukaryotic nucleus is organized into functional domains by scaffold or matrix attachment regions (S/MARs). These regions have previously been predicted to have a high potential for stress-induced duplex destabilization (SIDD). Here we report the parallel results of binding (reassociation) and computational SIDD analyses for regions within the human interferon gene cluster on the short arm of chromosome 9 (9p22). To verify and further refine the biomathematical methods, we focus on a 10 kb region in the cluster with the pseudogene IFNWP18 and the interferon alpha genes IFNA10 and IFNA7. In a series of S/MAR binding assays, we investigate the promoter and termination regions and additional attachment sequences that were detected in the SIDD profile. The promoters of the IFNA10 and the IFNA7 genes have a moderate approximately 20% binding affinity to the nuclear matrix; the termination sequences show stronger association (70-80%) under our standardized conditions. No comparable destabilized elements were detected flanking the IFNWP18 pseudogene, suggesting that selective pressure acts on the physicochemical properties detected here. In extended, noncoding regions a striking periodicity is found of rather restricted SIDD minima with scaffold binding potential. By various criteria, the underlying sequences represent a new class of S/MARs, thought to be involved in a higher level organization of the genome. Together, these data emphasize the relevance of SIDD calculations as a valid approach for the localization of structural, regulatory, and coding regions in the eukaryotic genome.

Fatal connections: when DNA ends meet on the nuclear matrix

A damaged nucleus has long been regarded simply as a "bag of broken chromosomes," with the DNA free ends moving around and forming connections with randomly encountered partners. Recent evidence shows this picture to be fundamentally wrong. Chromosomes occupy specific nuclear domains within which only limited movement is possible. In a human diploid nucleus, 6.6 x 10(9) base pairs (bp) of DNA are compartmentalized into chromosomes in a way that allows stringent control of replication, differential gene expression, recombination and repair. Most of the chromatin is further organized into looped domains by the dynamic binding of tethered bases to a network of intranuclear proteins, the so-called nuclear scaffold or matrix. Thus, DNA movement is severely curtailed, which limits the number of sites where interchanges can occur. This intricate organizational arrangement may render the genome vulnerable to processes that interfere with DNA repair. Both lower and higher eukaryotic cells perform homologous recombination (HR) and illegitimate recombination (IR) as part of their survival strategies. The repair processes comprising IR must be understood in the context of DNA structural organization, which is fundamentally different in prokaryotic and eukaryotic genomes. In this paper we first review important cellular processes including recombination, DNA repair, and apoptosis, and describe the central elements involved. Then we review the different DNA targets of recombination, and present recent evidence implicating the nuclear matrix in processes which can induce either repair, translocation, deletion, or apoptosis. J. Cell. Biochem. Suppl. 35:3-22, 2000.

Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements)

For a long time S/MARs could only be characterized by the assays in vitro that led to their detection. Only recently a number of biological activities emerged that are common to most or all S/MARs that are detected by the classic procedures. This review focuses on the phenomenon of transcriptional augmentation that is found for genomically anchored or episomal genes and on a group of partially overlapping activities that are suited to maintain an episomal status. Further, it is attempted to correlate properties of the S/MAR-scaffold interaction with prominent or prototype protein binding partners.

Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions

S/MARs are DNA elements 300 to several thousand base-pairs long, which are operationally defined by their affinity for the nuclear scaffold or matrix. S/MARs occur exclusively in eukaryotic genomes, where they mediate several functions. Because S/MARs do not have a clearcut consensus sequence, the characteristics that define their activity are thought to be structural. Ubiquitous S/MAR binding proteins have been identified, but to date no unique binding sequence or structural motif has been found. Here we show by computational analysis that S/MARs conform to a specific design whose essential attribute is the presence of stress-induced base-unpairing regions (BURs). Stress-induced destabilization (SIDD) profiles are calculated using a previously developed statistical mechanical procedure in which the superhelical deformation is partitioned between strand separation, twisting within denatured regions, and residual superhelicity. The results of these calculations show that BURs exhibit a succession of evenly spaced destabilized sites that would render part or all of the S/MAR sequence single stranded at sufficient superhelicity. These analyses are performed for a range of sequenced S/MAR elements from the borders of eukaryotic gene domains, from centromeres, and from positions where S/MARs are known to support the action of an enhancer. The results reported here are in excellent agreement with earlier in vitro chemical reactivity studies. This approach demonstrates the potential for computational analysis to predict the points of division of the eukaryotic genome into functional units (domains), and also to locate certain cis-regulatory sequences.

Hen's teeth and whale's feet: generalized characters and their compatibility

We propose a new model of computation for deriving phylogenetic trees based upon a generalization of qualitative characters. The model we propose is based upon recent experimental research in molecular biology. We show that the general case of determining perfect compatibility of generalized ordered characters is an NP-complete problem, but can be solved in polynomial time for a special case.

In vivo decay kinetic parameters of hammerhead ribozymes

Ribozymes offer a potentially important way to inactivate intracellular RNA from almost any gene whose nucleotide sequence is known. Recently, we found that hammerhead ribozymes directed against mRNA of tumour necrosis factor alpha (TNF alpha) and its derivatives, preferentially bind to a cellular protein(s). To better understand the effect of different 3'-terminal hairpins on ribozyme stability as well as their effect on the protein binding to the ribozyme, a mathematical treatment of the decay of three TNF alpha ribozymes that differed at their 3' ends was performed. One ribozyme contained a 3'-terminal hairpin derived from a transcription terminator of bacteriophage T7, another contained the same hairpin but modified to be highly enriched for G+C nucleotides, and a third lacked a hairpin. The TNF alpha ribozyme decay had two kinetic components. The slow component exhibited exponential decay with a half life of approximately 250 h in all cases. The 3'-terminal hairpin has no significant effect on this component. This slow phase accounted for 60-80% of ribozyme decay. The rapid phase also exhibited exponential decay. For this phase, a 3'-terminal hairpin roughly doubled the half-life (1.7-3.4). The slow phase of degradation was about three times faster for a ribozyme directed at the integrase mRNA of human immunodeficiency virus-1 than that seen with the TNF alpha ribozyme. Taken together, these results suggest that the ribozyme population is initially sensitive to degradation, with the presence of a hairpin provides some protection, and indicate that the addition of the hairpin to the ribozyme did not prevent the in vivo additional stabilizing effect of the protein(s).

An influenza virus containing nine different RNA segments

The packaging mechanism of segmented RNA viruses has not been well studied. Specifically, it has not been clear whether influenza A viruses package only eight RNA segments or whether virus particles contain more than eight segments. Using a newly developed ribonucleoprotein (RNP) transfection method, we engineered an influenza virus which must contain nine different RNA segments rather than the usual eight in order to survive under the experimental growth conditions. This result is compatible with a mechanism of packaging which allows influenza virus to encapsidate more than eight RNA segments. We also suggest that the virus packages its RNAs randomly and that this random packaging results in infectious viruses with the required ("right") complement of RNA segments.