Ontogeny influences sensitivity to climate change stressors in an endangered fish.

Coastal ecosystems are among the most human-impacted habitats globally, and their management is often critically linked to recovery of declining native species. In the San Francisco Estuary, the Delta Smelt (Hypomesus transpacificus) is an endemic, endangered fish strongly tied to Californian conservation planning. The complex life history of Delta Smelt combined with dynamic seasonal and spatial abiotic conditions result in dissimilar environments experienced among ontogenetic stages, which may yield stage-specific susceptibility to abiotic stressors. Climate change is forecasted to increase San Francisco Estuary water temperature and salinity; therefore, understanding the influences of ontogeny and phenotypic plasticity on tolerance to these critical environmental parameters is particularly important for Delta Smelt and other San Francisco Estuary fishes. We assessed thermal and salinity limits in several ontogenetic stages and acclimation states of Delta Smelt, and paired these data with environmental data to evaluate sensitivity to climate-change stressors. Thermal tolerance decreased among successive stages, with larval fish exhibiting the highest tolerance and post-spawning adults having the lowest. Delta Smelt had limited capacity to increase tolerance through thermal acclimation, and comparisons with field temperature data revealed that juvenile tolerance limits are the closest to current environmental conditions, which may make this stage especially susceptible to future climate warming. Maximal water temperatures observed in situ exceeded tolerance limits of juveniles and adults. Although these temperature events are currently rare, if they increase in frequency as predicted, it could result in habitat loss at these locations despite other favourable conditions for Delta Smelt. In contrast, Delta Smelt tolerated salinities spanning the range of expected environmental conditions for each ontogenetic stage, but salinity did impact survival in juvenile and adult stages in exposures over acute time scales. Our results underscore the importance of considering ontogeny and phenotypic plasticity in assessing the impacts of climate change, particularly for species adapted to spatially and temporally heterogeneous environments

Sociodemographic predictors of residents worry about contaminated sites

© 2018 Elsevier B.V. The management and remediation of contaminated environments increasingly involves engagement with affected local residents. Of late, risk communication tools and guidelines have drawn attention to the stress and concern of residents as a result of heightened awareness of localised contamination and the need to address these less visible impacts of contamination when engaging with affected communities. Despite this emerging focus, there is an absence of research exploring the factors that predict resident worry about neighbourhood contamination. This paper aims to address this shortcoming by drawing on data from a cross-sectional survey of 2009 adult residents in neighbourhoods near 13 contaminated sites across Australia. Ordered logistic regression was used to determine the sociodemographic, environmental, and knowledge-based factors that influence residents’ degree of worry. The findings suggest age, gender and income significantly affect residents’ degree of worry. Being knowledgeable about the contaminant and having a stronger perception of a sense of place within a particular neighbourhood were associated with lower degrees of worry. Type of contaminant also impacted resident worry, with residents being less likely to worry about solvents and metals than other types of contaminants. Our analyses suggest resident worry can be reduced through improving access to accurate information and the development of specific risk reduction strategies tailored to each neighbourhood and aimed at the heterogeneous distribution of worry amongst residential populations

The secretome of alginate-encapsulated limbal epithelial stem cells modulates corneal epithelial cell proliferation

Limbal epithelial stem cells may ameliorate limbal stem cell deficiency through secretion of therapeutic proteins, delivered to the cornea in a controlled manner using hydrogels. In the present study the secretome of alginate-encapsulated limbal epithelial stem cells is investigated. Conditioned medium was generated from limbal epithelial stem cells encapsulated in 1.2% (w/v) calcium alginate gels. Conditioned medium proteins separated by 1-D gel electrophoresis were visualized by silver staining. Proteins of interest including secreted protein acidic and rich in cysteine, profilin-1, and galectin-1 were identified by immunoblotting. The effect of conditioned medium (from alginate-encapsulated limbal epithelial stem cells) on corneal epithelial cell proliferation was quantified and shown to significantly inhibit (P</=0.05) their growth. As secreted protein acidic and rich in cysteine was previously reported to attenuate proliferation of epithelial cells, this protein may be responsible, at least in part, for inhibition of corneal epithelial cell proliferation. We conclude that limbal epithelial stem cells encapsulated in alginate gels may regulate corneal epithelialisation through secretion of inhibitory proteins

Influence of elastase on alanine-rich peptide hydrogels

The self-assembly of the alanine-rich amphiphilic peptides Lys(Ala)6Lys (KA6K) and Lys(Ala)6Glu (KA6E)with homotelechelic or heterotelechelic charged termini respectively has been investigated in aqueous solution. These peptides contain hexa-alanine sequences designed to serve as substrates for the enzyme elastase. Electrostatic repulsion of the lysine termini in KA6K prevents self-assembly, whereas in contrast KA6E is observed, through electron microscopy, to form tape-like fibrils, which based on X-ray scattering contain layers of thickness equal to the molecular length. The alanine residues enable efficient packing of the side-chains in a beta-sheet structure, as revealed by circular dichroism, FTIR and X-ray diffraction experiments. In buffer, KA6E is able to form hydrogels at sufficiently high concentration. These were used as substrates for elastase, and enzyme-induced de-gelation was observed due to the disruption of the beta-sheet fibrillar network. We propose that hydrogels of the simple designed amphiphilic peptide KA6E may serve as model substrates for elastase and this could ultimately lead to applications in biomedicine and regenerative medicine

Decision making for net zero policy design and climate action:Considerations for improving translation at the research-policy interface: A UK Carbon Dioxide Removal Case Study

The impacts of climate change on society and the natural environment are being experienced now, with extreme weather events increasing in frequency and severity across the globe. To keep the Paris Agreement's ambition of limiting warming to 1.5ºC above pre-industrial levels there is now also a need to establish and scale a new sector to remove CO2 at Giga-tonne scale for over a century. Despite this mounting evidence and warnings, current climate policy in the UK and globally falls far short of achieving the required reductions in CO2 emissions or establishment of a new removal sector needed to stave off the risks posed by climate change. Some of the science on climate risk is abundant and well evidenced, but the policy response is lacking in effectiveness. Other evidence to design policy, such as Carbon Dioxide Removal (CDR), is fraught with deep uncertainty. Why are the plethora of scientific evidence, assessments and decision support tools available to decision and policymakers not always translating into effective climate-net zero policy action? How can emergent evidence be brought in introduced to shape new sectors such as CDR? What are the capacity gaps? Through a combination of literature review, interviews and UK policy workshops over 17 months these are some of the questions that this contribution sought insight. We set out three recommendations for policymakers and other stakeholders, including academic researchers and third sector organisations, to address the identified gaps associated with translating climate risk and net zero decision support into effective climate policy: Enhance collaboration between decision-makers, policymakers, analysts, researchers, and other stakeholders to co-develop and co-design operational climate risk assessments and policies, relevant to context. Identify the research and capacity gaps around climate risk decision-making under uncertainty, and work with stakeholders across the decision value chain to ensure those gaps are addressed. Co-create effective translation mechanisms to embed decision-support tools into policy better, employing a participatory approach to ensure inclusion of diverse values and viewpoints. It is fundamental that there is improvement in our understanding about how we can make good decisions and operationalise them, rather than simply focus on further research on the climate risk and net zero problem

Decision making for net zero policy design and climate action:Considerations for improving translation at the research-policy interface: A UK Carbon Dioxide Removal Case Study

The impacts of climate change on society and the natural environment are being experienced now, with extreme weather events increasing in frequency and severity across the globe. To keep the Paris Agreement's ambition of limiting warming to 1.5ºC above pre-industrial levels there is now also a need to establish and scale a new sector to remove CO2 at Giga-tonne scale for over a century. Despite this mounting evidence and warnings, current climate policy in the UK and globally falls far short of achieving the required reductions in CO2 emissions or establishment of a new removal sector needed to stave off the risks posed by climate change. Some of the science on climate risk is abundant and well evidenced, but the policy response is lacking in effectiveness. Other evidence to design policy, such as Carbon Dioxide Removal (CDR), is fraught with deep uncertainty. Why are the plethora of scientific evidence, assessments and decision support tools available to decision and policymakers not always translating into effective climate-net zero policy action? How can emergent evidence be brought in introduced to shape new sectors such as CDR? What are the capacity gaps? Through a combination of literature review, interviews and UK policy workshops over 17 months these are some of the questions that this contribution sought insight. We set out three recommendations for policymakers and other stakeholders, including academic researchers and third sector organisations, to address the identified gaps associated with translating climate risk and net zero decision support into effective climate policy: Enhance collaboration between decision-makers, policymakers, analysts, researchers, and other stakeholders to co-develop and co-design operational climate risk assessments and policies, relevant to context. Identify the research and capacity gaps around climate risk decision-making under uncertainty, and work with stakeholders across the decision value chain to ensure those gaps are addressed. Co-create effective translation mechanisms to embed decision-support tools into policy better, employing a participatory approach to ensure inclusion of diverse values and viewpoints. It is fundamental that there is improvement in our understanding about how we can make good decisions and operationalise them, rather than simply focus on further research on the climate risk and net zero problem

A spectroscopic search for faint secondaries in cataclysmic variables

The secondary in cataclysmic variables (CV's) is usually detected by cross-correlation of the CV spectrum with that of a K or M dwarf template, to produce a radial velocity curve. Although this method has demonstrated its power, it has its limits in the case of noisy spectra, such as are found when the secondary is faint. A method of co-adding spectra, called skew mapping, has been proposed in the past. Gradually, examples of its application are being published. Nonetheless, so far no journal article has described the technique in detail. To answer this need, this paper explores in detail the capabilities of skew mapping when determining the amplitude of the radial velocity for faint secondaries. It demonstrates the method's power over techniques that are more conventional, when the signal-to-noise (s/n) ratio is poor. The paper suggests an approach to assessing the quality of results. This leads in the case of the investigated objects to a first tier of results, where we find K2=127+-23 km/s for SY Cnc, K2=144+-18 km/s for RW Sex, and K2=262+-14 km/s for UX UMa. These we believe to be the first direct determinations of K2 for these objects. Furthermore, we also obtain K2=263+-30 km/s for RW Tri, close to a skew mapping result obtained elsewhere. In the first three cases, we use these results to derive the mass of the white dwarf companion. A second tier of results includes UU Aqr, EX Hya, and LX Ser, for which we propose more tentative values of K2. Clear failures of the method are also discussed (EF Eri, VV Pup, SW Sex).Comment: 23 pages, 22 figures, 10 tables; translated to pdf from a Word file - no TeX version available. Accepted for publication in MNRA

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no ^(15)NH^+_4 assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living’ population, and are not dependent on methane or ANME activity. We investigated the possibility of N_2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. ^(15)N_2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, ^(15)N_2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced ^(15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations

Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH₄ and ¹⁵N₂ revealed differences in cellular ¹⁵N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in ¹⁵N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph