When the Background Matters: Using Scenarios from Integrated Assessment Models in Prospective Life Cycle Assessment

Prospective life cycle assessment (LCA) needs to deal with the large epistemological uncertainty about the future to support more robust future environmental impact assessments of technologies. This study proposes a novel approach that systematically changes the background processes in a prospective LCA based on scenarios of an integrated assessment model (IAM), the IMAGE model. Consistent worldwide scenarios from IMAGE are evaluated in the life cycle inventory using ecoinvent v3.3. To test the approach, only the electricity sector was changed in a prospective LCA of an internal combustion engine vehicle (ICEV) and an electric vehicle (EV) using six baseline and mitigation climate scenarios until 2050. This case study shows that changes in the electricity background can be very important for the environmental impacts of EV. Also, the approach demonstrates that the relative environmental performance of EV and ICEV over time is more complex and multifaceted than previously assumed. Uncertainty due to future developments manifests in different impacts depending on the product (EV or ICEV), the impact category, and the scenario and year considered. More robust prospective LCAs can be achieved, particularly for emerging technologies, by expanding this approach to other economic sectors beyond electricity background changes and mobility applications as well as by including uncertainty and changes in foreground parameters. A more systematic and structured composition of future inventory databases driven by IAM scenarios helps to acknowledge epistemological uncertainty and to increase the temporal consistency of foreground and background systems in LCAs of emerging technologies.     

On the Detection of Unusual Points in Regression

Some procedures, based on studentized residuals and the diagonal elements of the ‘hat’ matrix, for the detection of unusual points in regression are discussed. These procedures are quite simple but effective to uncover unusual structure of the data. Some examples are given.     

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.     

罗汉果组培繁殖的技术要点

报道罗汉果组培繁殖的各项主要技术要点,包括组培条件、培养基的配制、外植体的选取与消毒、接种与培养、种源保存、炼苗与移栽、苗木包装与运输等。提出了5种培养基参考配方,即茎段诱导培养:MS+BA0.5～1.0mg/L+IAA(NAA)0.05～0.1mg/L+白糖3%+琼脂4.5g/L,pH5.8;茎尖诱导培养:MS+BA0.5～1.0mg/L+NAA0.05～0.1mg/L+椰子水100mL+白糖3%+琼脂4.5mg/L,pH5.8;继代培养(丛生芽方式):MS+BA0.3～0.7mg/L+NAA0.05/IAA0.1mg/L+白糖3%+琼脂4.5mg/L,pH5.8;继代培养(微型扦插方式):MS+BA0.1mg/L+IAA0.3mg/L+活性炭0.07g/L+白糖3%+琼脂4.5mg/L,pH5.8;生根培养:MS+BA0.07mg/L+IBA0.15mg/L+IAA0.1mg/L+活性炭0.1g/L+白糖3%+琼脂4.5mg/L,pH5.8。分析了外植体培养过程中可能出现的不良状况的原因并提出预防措施,明确了炼苗移栽的适宜条件并制定出相应的管理方法。形成了一套较为完整的罗汉果组培苗繁殖生产技术规程。     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

Temperature dependence of predation depends on the relative performance of predators and prey

The temperature dependence of predation rates is a key issue for understanding and predicting the responses of ecosystems to climate change. Using a simple mechanistic model, we demonstrate that differences in the relative performances of predator and prey can cause strong threshold effects in the temperature dependence of attack rates. Empirical data on the attack rate of northern pike (Esox lucius) feeding on brown trout (Salmo trutta) confirm this result. Attack rates fell sharply below a threshold temperature of +11°C, which corresponded to a shift in relative performance of pike and brown trout with respect to maximum attack and escape swimming speeds. The average attack speed of pike was an order of magnitude lower than the escape speed of brown trout at 5°C, but approximately equal at temperatures above 11°C. Thresholds in the temperature dependence of ecological rates can create tipping points in the responses of ecosystems to increasing temperatures. Thus, identifying thresholds is crucial when predicting future effects of climate warming.     

Decision errors in evaluating tipping points for ecosystem resilience

When an ecosystem reaches tipping points for selected indicators, resilience to further changes in external drivers can decrease, regime shifts can occur that diminish the capacity of the ecosystem to provide ecosystem services, and the ecosystem is more vulnerable to collapse. Evaluating tipping points for resilience using crisp decision rules can result in decision errors about whether or not resilience has been compromised. The source and nature of those errors are described and a fuzzy decision rule is proposed for evaluating resilience. Decision errors are evaluated for four cases. Cases 1 through 3 (or case 4) derive conditions for evaluating decision errors when there is a single (or multiple) indicator(s). The primary sources of decision errors for the four cases are discrepancies between measured (or established) and true values of the indicators (or tipping points) and using a crisp decision rule to reach conclusions about whether or not resilience has been compromised. A fuzzy decision rule, based on fuzzy TOPSIS, is proposed that evaluates the extent to which an ecosystem is resilient. Although crisp decision rules provide unambiguous conclusions about resilience, those conclusions can be faulty, particularly when measured indicators and established tipping points deviate substantially from their true values. In contrast, the conclusions from the fuzzy decision rule are less susceptible to the decision errors and, hence, faulty decisions.     

Probleme der Erweiterung der Prüfverteilungen des Maximum-Modulus-Testes und des DUNNETT-Testes

SCHULZ (1976) gave formulas for the approximate computation of the percentage points needed for the comparison of sample means by the Maximum-Modulus-Test resp. by the DUNNETT-Test. Our investigation shows that these formulas are also practicable if the number of the mean differences k is greater than 20. The maximum difference between the exact values and the approximate values of the percentage points amounts to 0,05 in the case of the Maximum-Modulus-Test with k >20 and degrees of freedom v > k for a level of error a = 0,05 resp. a = 0,01. In the case of the DUNNETT-Test this maximum difference amounts to 0,02 for 20 < k < 50 and a = 0,05. Besides it can be here supposed that the approximate percentage points are also practicable for both k >50, a = 0,05 and k >20, a = 0,01.     

MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics

Identifying protein–protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an “abortive” biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity-dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist. Here we modified the structure of BioID2, derived from Aquifex aeolicus BirA, to create a smaller, highly active, biotin ligase that we named MicroID2. Truncation of the C terrminus of BioID2 and addition of mutations to alleviate blockage of biotin/ATP binding at the active site of BioID2 resulted in a smaller and highly active construct with lower background labeling. Several additional point mutations improved the function of our modified MicroID2 construct compared with BioID2 and other biotin ligases, including TurboID and miniTurbo. MicroID2 is the smallest biotin ligase reported so far (180 amino acids [AAs] for MicroID2 versus 257 AAs for miniTurbo and 338 AAs for TurboID), yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurbo. MicroID2 also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we in addition developed a MicroID2 mutant, termed lbMicroID2 (low background MicroID2), that has lower labeling efficiency but significantly reduced biotin scavenging compared with BioID2. Finally, we demonstrate utility of MicroID2 in mass spectrometry experiments by localizing MicroID2 constructs to subcellular organelles and measuring proximal interactions.     

State-space modeling clarifies productivity regime shifts of Japanese flying squid

Regime shifts of climatic and environmental conditions potentially affect the productivity of fishery resources, posing challenges in stock management. The stocks of the Japanese flying squid (Todarodes pacificus) are suspected to suffer from regime shifts, but detecting the occurrence of regime shifts in this species is generally difficult and unreliable because the short-lived nature of this species inherently confounds the effect of regime shifts with observation and process errors. Here we developed a new state-space assessment model to evaluate the influence of regime shifts on the spawner-recruit relationship of the Japanese flying squid. The model simultaneously estimates the population dynamics of multiple stocks that could share some life history parameters, thereby stabilizing parameter inference. We demonstrate that two regime shifts in productivity around 1991 and 2015 caused two- to threefold changes of maximum sustainable yields. The model with regime shifts clarifies the relationship between fishing pressure and spawner abundance that is difficult to detect in a model with no regime shift. The state-space approach is a promising tool for accurately assessing stock status by separating the recruitment process from observation errors and is expected to contribute to the effective management of marine biological resources sensitive to regime shifts.