Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Three research priorities for just and sustainable urban systems: Now is the time to refocus

Now is the time to refocus efforts in urban research and design. A changing climate and extreme weather events are presenting unique challenges to urban systems around the world. These challenges illuminate the social barriers that accompany disruptive events such as resource inequities and injustices. In this perspective, we provide three research priorities for just and sustainable urban systems that help to address these matters. The three research priorities are: (1) social equity and justice, (2) circularity, and (3) digital twins. Conceptual context and future research directions are provided for each. For social equity and justice, the future directions are mandatory equity analysis and inclusionary practices, understanding and reconciling historical injustices, and intentional integration with diverse community stakeholders. For circularity applications, they are better metrics for integration, more robust evaluation frameworks, and dynamic modeling at multiple spatial and temporal scales. Future directions for digital twins include developing principles to reduce complexity, integrating model and system components, and reducing barriers to data access. These research priorities are core to meeting several of the United Nations Sustainable Development Goals (i.e., 1—No Poverty, 8—Decent Work and Economic Growth, 10—Reduced Inequalities, and 11—Sustainable Cities and Communities). Useful social and technical matters are discussed throughout, where we highlight the importance of prioritizing localized research efforts, provide guidance for community-engaged research and co-development practices, and explain how these priorities interact to align with the evolving field of industrial ecology.     

Grassland birds and rotational-grazing in the northeast: Breeding ecology,survival and management opportunities

We studied long-term (2002–2009) demographics of bobolinks (Dolichonyx oryzivorus) and savannah sparrows (Passerculus sandwichensis) breeding in rotationally grazed systems in the northeastern United States. Both nest success (6–44% bobolink; 7–48% savannah sparrow) and annual productivity (0.43–2.83 bobolink; 0.70–2.35 savannah sparrow) varied annually. Predation (48%) and trampling by cows (32%) accounted for most failed nests. Annual adult apparent survival ranged from 23% to 85% and showed substantial variation by species and sex. Although grazing resulted in substantial loss of vegetative cover, savannah sparrows responded similarly to predation and grazing-induced nest failure (time to renest, distance moved between nests) and generally remained in the same paddock to renest. Minimum paddock size to accommodate one female within this rotation was 70 m × 70 m (0.49 ha), allowing a female to stay within a paddock and move (approx. 50 m) between nesting attempts. To balance pasturing objectives and birds' needs in paddocks first grazed before 25 June, managers in the Northeast should rest that paddock 42–50 days before the second grazing. © 2011 The Wildlife Society.     

Stochastic exits from dormancy give rise to heavy‐tailed distributions of descendants in bacterial populations

Variance in reproductive success is a major determinant of the degree of genetic drift in a population. While many plants and animals exhibit high variance in their number of progeny, far less is known about these distributions for microorganisms. Here, we used a strain barcoding approach to quantify variability in offspring number among replicate bacterial populations and developed a Bayesian method to infer the distribution of descendants from this variability. We applied our approach to measure the offspring distributions for five strains of bacteria from the genus Streptomyces after germination and growth in a homogenous laboratory environment. The distributions of descendants were heavy‐tailed, with a few cells effectively ‘winning the jackpot’ to become a disproportionately large fraction of the population. This extreme variability in reproductive success largely traced back to initial populations of spores stochastically exiting dormancy, which provided early‐germinating spores with an exponential advantage. In simulations with multiple dormancy cycles, heavy‐tailed distributions of descendants decreased the effective population size by many orders of magnitude and led to allele dynamics differing substantially from classical population genetics models with matching effective population size. Collectively, these results demonstrate that extreme variability in reproductive success can occur even in growth conditions that are far more homogeneous than the natural environment. Thus, extreme variability in reproductive success might be an important factor shaping microbial population dynamics with implications for predicting the fate of beneficial mutations, interpreting sequence variability within populations and explaining variability in infection outcomes across patients.     

Extended Producer Responsibility in Thailand

Waste electrical and electronic equipment (WEEE) sheds light on the dimmer side of production and consumption patterns in modern societies. The rapid increase in its quantity and complexity contribute to the challenges it poses to solid waste management systems. Several members of the Organisation for Economic Co‐operation and Development (OECD) have relied on the principle of extended producer responsibility (EPR) to tackle the issue, with varying degrees of success. Several non‐OECD countries, including Thailand, are now developing WEEE programs and are looking for lessons from these first movers. This case study aims to provide an understanding both of this context and of the EPR program for WEEE proposed for Thailand. It finds that EPR mechanisms in general, and the proposed buy‐back system financed by product fees in Thailand in particular, have a strong potential to consolidate WEEE collection for the formal recycling sector by offering end users monetary incentives. On the negative side, this is an expensive combination of policy instruments, and the institutional design of the governmental fund is rigid. The policy proposal also contains no mechanism for product redesign—one of the objectives in the national WEEE strategy. This article suggests that the effectiveness of the policy might benefit from more flexibility at the compliance scheme level, in order to lessen the monopoly of the governmental fund, as well as the introduction of differentiated fees to promote environmentally friendly products.     

Environmental control and spatial structures in peatland vegetation

Question: What are the relative influences of environment and space in structuring the plant composition in a peatland complex? Location: Lakkasuo, southern boreal zone, Finland. Method: We used principal coordinates of neighbour matrices (PCNM) to model spatial structures in the plant composition of a peatland complex comprising ombrotrophic and minerotrophic, open and forested areas. We used redundancy analyses (RDA) and variation partitioning to assess the relative influences of chemical variables (peat and water characteristics), physical variables (hydrology, soil properties, shade), as well as broad‐scale (>350 m) and medium‐scale (100–350 m) spatial structures on vegetation assemblages. Results: We identified five different significant spatial patterns circumscribing (1) the minerotrophic–ombrotrophic gradient; (2) dry ombrotrophic and wet minerotrophic areas; (3) open and shaded areas; (4) dry open/shaded and wet patches within the ombrotrophic areas; and (5) dry open patches and dry forested patches. With spatial structures and environmental variables, we were able to model 30% of the variability in plant composition in the peatland complex, 13% of which was attributable to spatial structures alone. Conclusions: We demonstrated that in the peatland complex, the spatial dependence processes were more important at the broadest scale, and found that patterns at a medium scale might reflect finer‐scale patterns that were not investigated here. Spatial autocorrelation in vegetation composition in the peatland complex appeared to be driven by Sphagnum species. Our results emphasize that spatial modelling should be routinely implemented in studies looking at species composition, since they significantly increase the explained proportion of variance.     

Ontogenetic Variation in the Diurnal Food and Habitat Associations of an Endemic and an Exotic Fish in Floodplain Ponds: Consequences for Niche Partitioning

In floodplain ponds with low piscivore abundance, both endemic Midgley's gudgeons, Hypseleotris sp. 5, and exotic mosquitofish, Gambusia holbrooki, showed significant ontogenetic variation in the use of food and space. Small gudgeons were generally associated with surface and benthic habitats, then restricted their distribution to benthic habitats at a size of approximately 24mm (standard length). The ontogenetic variation in mosquitofish habitat use was less discrete, and could be described as a tendency for larger individuals to be associated with the bottom of the littoral macrophyte beds than with the surface of the macrophyte beds or surface of the limnetic zone. Small gudgeons exhibited high spatial overlap with mosquitofish within the surface habitats of the ponds. All size-class/species comparisons showed significant partitioning of food resources, however, the diets of small gudgeons and mosquitofish were very similar. Therefore, juvenile gudgeons may have to pass through a similar spatial and trophic niche to introduced mosquitofish before recruiting to the adult stage. Possible mechanisms driving the ontogenetic variation in gudgeon and mosquitofish habitat use are discussed. This paper demonstrates that ontogenetic niche shifts at fine spatial scales can affect our interpretation of interactions between native and introduced fishes.     

Stable carbon isotope ratios for the gray whale (<Emphasis Type="Italic">Eschrichtius robustus</Emphasis>) in the breeding grounds of Baja California Sur,Mexico

This work investigated the feeding ecology and behaviour of gray whales in Bahía Magdalena. Underwater observations of bottom feeding were made (n=4). Skin biopsies of the gray whale had a carbon isotope value of –16.5 ± 0.1 (range from –16.4 to –16.7, n=7). Prey in Bahía Magdalena had a carbon isotope value of –18.4. Dietary enrichment from prey in Bahía Magdalena would correspond to 2 ± 0.1, whereas previously published results for prey in Alaska would result in an enrichment of 3, which suggests that whales were more likely feeding on prey from Bahía Magdalena. Carbon isotopic oscillation along the baleen plate of a stranded 1-year-old whale showed a variation in diet during the year, which suggests continual feeding during this time and corresponding to dietary sample measurements from Bahía Magdalena in winter and Alaska in summer.     

Charging up Battery Recycling Policies: Extended Producer Responsibility for Single‐Use Batteries in the European Union,Canada, and the United States

Extended producer responsibility (EPR) policies have proven effective at raising consumer awareness, expanding waste collection infrastructure, and shifting costs of end‐of‐life (EOL) management from municipalities to stewardship organizations. Yet, such policies have been less successful in advancing waste management programs that ensure a net environmental benefit. This article analyzes how EPR policies for single‐use batteries in the European Union (EU), Canada, and the United States address the environmental costs and benefits of EOL management. Considering these EPR policies is instructive, because single‐use batteries have high collection costs and are of relatively low economic value for waste processors. Without deliberate planning, the environmental burdens of collecting and recycling such batteries may exceed the benefits. This article considers how EPR policies for single‐use batteries integrate performance requirements such as collection rates, recycling efficiencies, and best available techniques. It argues that for such policies to be effective, they need to be extended to address waste collection practices, the life cycle consequences of EOL management, and the quality of recovered materials. Such strategies are relevant to EPR policies for other products with marginal secondary value, including some textiles, plastics, and other types of electronic waste.