Lipid-anchored Synaptobrevin Provides Little or No Support for Exocytosis or Liposome Fusion

SNARE proteins catalyze many forms of biological membrane fusion, including Ca²⁺-triggered exocytosis. Although fusion mediated by SNAREs generally involves proteins anchored to each fusing membrane by a transmembrane domain (TMD), the role of TMDs remains unclear, and previous studies diverge on whether SNAREs can drive fusion without a TMD. This issue is important because it relates to the question of the structure and composition of the initial fusion pore, as well as the question of whether SNAREs mediate fusion solely by creating close proximity between two membranes versus a more active role in transmitting force to the membrane to deform and reorganize lipid bilayer structure. To test the role of membrane attachment, we generated four variants of the synaptic v-SNARE synaptobrevin-2 (syb2) anchored to the membrane by lipid instead of protein. These constructs were tested for functional efficacy in three different systems as follows: Ca²⁺-triggered dense core vesicle exocytosis, spontaneous synaptic vesicle exocytosis, and Ca²⁺-synaptotagmin-enhanced SNARE-mediated liposome fusion. Lipid-anchoring motifs harboring one or two lipid acylation sites completely failed to support fusion in any of these assays. Only the lipid-anchoring motif from cysteine string protein-α, which harbors many lipid acylation sites, provided support for fusion but at levels well below that achieved with wild type syb2. Thus, lipid-anchored syb2 provides little or no support for exocytosis, and anchoring syb2 to a membrane by a TMD greatly improves its function. The low activity seen with syb2-cysteine string protein-α may reflect a slower alternative mode of SNARE-mediated membrane fusion.     

Negative range size–abundance relationships in Indo‐Pacific bird communities

The positive relationship between range size and abundance is one of the best‐documented patterns in macroecology, but a growing number of studies from isolated tropical areas have reported negative or neutral relationships. It has been hypothesized that the combination of geographic isolation and environmental stability create selection pressures that favor narrowly specialized species, which could drive these non‐positive relationships. To test this idea, we measured the range size–abundance relationships of eleven bird communities in mature and degraded forest on four islands in the Indo‐Pacific, namely Flores in the Lesser Sundas, Seram in the Moluccas, and the New Caledonian islands of Grande Terre and Lifou. Local abundance data was gathered through extensive and methodologically consistent surveying, and regressed against global range size using linear mixed effect models. The relationship between range size and abundance was significantly negative across all combined mature and degraded forest communities. As negative relationships were found in degraded forest with little environmental stability, we conclude that the abundance of small‐ranged species on the study islands cannot be ascribed to narrow specialization. Rather, cross‐habitat community comparisons indicate that locally abundant endemic and near‐endemic species adapted to a broad spectrum of local environmental conditions cause the observed negative relationships. We suspect that geographic isolation facilitates the evolution of species that are simultaneously broad‐niched, small‐ranged, and abundant, as water barriers limit the range expansions that would typically accompany species’ attainment of high local population densities. The consistently negative relationships found across Indo‐Pacific islands represent a striking deviation from the positive range size–abundance relationship ‘rule’, and future studies should seek to determine whether the patterns detected here extend to geographically isolated mainland environments.     

Tracing a bog-iron bloomery furnace in an adjacent lake-sediment record in Ängersjö, central Sweden,using pollen and geochemical signals

Recent studies of bloomery sites in Sweden indicate the amount of iron produced with this early low-technology smelter was greater than previously thought, which implies greater economic importance. Little is known about the history of bloomery technology, not least the timeframe over which individual bloomeries were operated, as well as their impact on the landscape because of resource consumption and pollution. In this study we performed pollen and geochemical analyses of the lake-sediment record from Rörtjärnen, which is 120 m from the remains of a documented bloomery [one radiocarbon date: ad 1300–1435 (1 σ)], in Ängersjö, Hälsingland. A surface-soil transect shows a limited geochemical signal only within 20 m of the bloomery, and the sediment pollen record provides little direct evidence of an active bloomery and is consistent with other studied sites in the area linked to forest grazing or cultivation. Instead, we find major changes in sediment geochemistry during ad 800–1200, centered on a unique peak in Pb at ad 1030–1060. These changes include, e.g., Si (biogenic) and P, together with changes in pollen (e.g., Betula, Picea, Cyperaceae), which together indicate disturbance in the forest and especially the adjoining fen. We attribute these changes to a period of bloomery-related activities predating the radiocarbon date of the charcoal from the bloomery, and suggest that date represents a late phase for the site.     

PSAMM: A Portable System for the Analysis of Metabolic Models

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies.     

Correction: Periconceptional Heat Stress of Holstein Dams Is Associated with Differences in Daughter Milk Production and Composition during Multiple Lactations

The fertility of lactating Holstein cows is severely reduced during periods of heat stress. Despite this reduction in fertility, however, some inseminations conducted during heat stress result in successful pregnancies from which heifer calves are born. Many of these heifer calves are retained and raised to enter the milking herd as replacement animals. Heat stress experienced by these females around the time they were conceived may confer long-lasting effects that alter subsequent milk production capacity. The objective of this study was to examine the relationship between periconceptional heat stress and subsequent milk production of primiparous cows. National Dairy Herd Improvement Association data was obtained from Dairy Records Management Systems. Records included Holstein cows that had completed at least one lactation in one of three states with large populations of dairy cattle and which are known for having hot, humid summers: Georgia, Florida or Texas. Dates of conception were calculated by subtracting 276 d from the recorded birth date of each individual cow. Records for cows conceived within the months of June, July, and August were retained as heat stress-conceived (HSC) cows (n = 94,440); cows conceived within the months of December, January, and February were retained as thermoneutral-conceived (TNC) contemporaries (n = 141,365). In order to account for the effects of environmental conditions on total milk production for a given lactation, cows were blocked by season of calving (winter, spring, summer or fall). Adjusted 305-day mature-equivalent milk production was evaluated with a mixed model ANOVA using SAS, in which random effects were used to account for variability between herds. Of the cows that calved in the summer, fall and winter, TNC cows had higher milk yield than the HSC cows in all states. Interestingly, the cows that calved in the spring presented a unique relationship, with HSC cows producing more milk. Overall however, heat stress at the time of conception is associated with lower milk production during the first lactation. While this association does not prove cause and effect, it does provide justification for additional investigation into whether heat stress around the time of conception results in long-term, detrimental consequences for the conceptus.     

Diel Surface Temperature Range Scales with Lake Size

Ecological and biogeochemical processes in lakes are strongly dependent upon water temperature. Long-term surface warming of many lakes is unequivocal, but little is known about the comparative magnitude of temperature variation at diel timescales, due to a lack of appropriately resolved data. Here we quantify the pattern and magnitude of diel temperature variability of surface waters using high-frequency data from 100 lakes. We show that the near-surface diel temperature range can be substantial in summer relative to long-term change and, for lakes smaller than 3 km², increases sharply and predictably with decreasing lake area. Most small lakes included in this study experience average summer diel ranges in their near-surface temperatures of between 4 and 7°C. Large diel temperature fluctuations in the majority of lakes undoubtedly influence their structure, function and role in biogeochemical cycles, but the full implications remain largely unexplored.