Research hypotheses have been a cornerstone of science since before Galileo. Many have argued that hypotheses (1) encourage discovery of mechanisms, and (2) reduce bias—both features that should ...increase transferability and reproducibility. However, we are entering a new era of big data and highly predictive models where some argue the hypothesis is outmoded. We hypothesized that hypothesis use has declined in ecology and evolution since the 1990s, given the substantial advancement of tools further facilitating descriptive, correlative research. Alternatively, hypothesis use may have become more frequent due to the strong recommendation by some journals and funding agencies that submissions have hypothesis statements. Using a detailed literature analysis (N = 268 articles), we found prevalence of hypotheses in eco–evo research is very low (6.7%–26%) and static from 1990–2015, a pattern mirrored in an extensive literature search (N = 302,558 articles). Our literature review also indicates that neither grant success nor citation rates were related to the inclusion of hypotheses, which may provide disincentive for hypothesis formulation. Here, we review common justifications for avoiding hypotheses and present new arguments based on benefits to the individual researcher. We argue that stating multiple alternative hypotheses increases research clarity and precision, and is more likely to address the mechanisms for observed patterns in nature. Although hypotheses are not always necessary, we expect their continued and increased use will help our fields move toward greater understanding, reproducibility, prediction, and effective conservation of nature.
We use a quantitative literature review to show that use of a priori hypotheses is still rare in the fields of ecology and evolution. We provide suggestions about the group and individual‐level benefits of hypothesis use.
The Hawaiian-Emperor hotspot track has a prominent bend, which has served as the basis for the theory that the Hawaiian hotspot, fixed in the deep mantle, traced a change in plate motion. However, ...paleomagnetic and radiometric age data from samples recovered by ocean drilling define an age-progressive paleolatitude history, indicating that the Emperor Sea-mount trend was principally formed by the rapid motion (over 40 millimeters per year) of the Hawaiian hotspot plume during Late Cretaceous to early-Tertiary times (81 to 47 million years ago). Evidence for motion of the Hawaiian plume affects models of mantle convection and plate tectonics, changing our understanding of terrestrial dynamics.
The value of non‐commodity ecosystem services provided by forests is widely recognized, but intensive forest management practices are increasing, with uncertain consequences for a multitude of these ...services. Quantitative relationships among biodiversity conservation, timber production and other ecosystem services remain poorly understood, especially during the early‐successional period of intensively managed forestlands.
We manipulated management intensity in regenerating forest plantations to test the prediction that treatments aimed at maximizing timber production decrease biodiversity conservation and non‐timber services. We measured species richness of 3 taxonomic groups and 13 proxies for provisioning, cultural and regulating services within stands randomly assigned to one of the three herbicide application intensities or an untreated control.
Herbicides increased allocation of net primary production to crop trees, increasing projected timber volume and revenues at 40‐ and 60‐year harvest ages. Commonly used herbicide prescriptions reduced culturally valued plants by 71%, wild‐ungulate forage by 41%, avian richness by 20% and pollinator floral resources by 42%, the latter being associated with 38% fewer pollinator species. However, agriculturally valued bumblebees, pollination of blueberries, avian‐mediated arthropod control, wild ungulate observations and regulation services tied to forest productivity appeared unaffected by increasing management intensity and timber production.
Species richness and flora‐provided services in young forest plantations exhibited strong trade‐offs with projected timber production, whereas post‐treatment vegetation regeneration and site‐level variation likely maintained a range of other services. Although vegetation recovery is important for supporting wildlife and some ecosystem services on industrial forestlands, it is unlikely that any single prescription can optimize both timber and non‐timber benefits to society across managed forest landscapes. Instead, producing different services in discrete portions of the landscape may be necessary.
Synthesis and applications. We tested the effects of intensive forest management via herbicides on ecosystem services and found that biodiversity responses and services from early‐successional vegetation trade‐off against timber production. A number of services appeared to be compatible with timber production, although no single prescription optimized the full range of services. Stand‐level biodiversity conservation and a variety of services could potentially be provided by treatment skips and less‐intensive management on productive sites, although it is unlikely that all services can be optimized without landscape‐level planning.
We tested the effects of intensive forest management via herbicides on ecosystem services and found that biodiversity responses and services from early‐successional vegetation trade‐off against timber production. A number of services appeared to be compatible with timber production, although no single prescription optimized the full range of services. Stand‐level biodiversity conservation and a variety of services could potentially be provided by treatment skips and less‐intensive management on productive sites, although it is unlikely that all services can be optimized without landscape‐level planning.
Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our ...understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.
The soil priming effect (PE), defined as the modification of soil organic matter decomposition by labile carbon (C) inputs, is known to influence C storage in terrestrial ecosystems. However, how ...chronic nutrient addition, particularly in leguminous and non-leguminous forests, will affect PE through interaction with nutrient (e.g., nitrogen and phosphorus) availability is still unclear. Therefore, we collected soils from leguminous and non-leguminous subtropical plantations across a suite of historical nutrient addition regimes. We added 13C-labeled glucose to investigate how background soil nutrient conditions and microbial communities affect priming and its potential microbial mechanisms. Glucose addition increased soil organic matter decomposition and prompted positive priming in all soils, regardless of dominant overstory tree species or fertilizer treatment. In non-leguminous soil, only combined nitrogen and phosphorus addition led to a higher positive priming than the control. Conversely, soils beneath N-fixing leguminous plants responded positively to P addition alone, as well as to joint NP addition compared to control. Using DNA stable-isotope probing, high-throughput quantitative PCR, enzyme assays and microbial C substrate utilization, we found that positive PE was associated with increased microbial C utilization, accompanied by an increase in microbial community activity, nutrient-related gene abundance, and enzyme activities. Our findings suggest that the balance between soil available N and P effects on the PE, was dependent on rhizosphere microbial community composition. Furthermore, these findings highlight the roles of the interaction between plants and their symbiotic microbial communities in affecting soil priming and improve our understanding of the potential microbial pathways underlying soil PEs.
The 'Solnhofen Limestone' beds of the Southern Franconian Alb, Bavaria, southern Germany, have for centuries yielded important pterosaur specimens, most notably of the genera Pterodactylus and ...Rhamphorhynchus. Here we describe a new genus of non-pterodactyloid pterosaur based on an extremely well preserved fossil of a young juvenile: Bellubrunnus rothgaengeri (gen. et sp. nov.).
The specimen was examined firsthand by all authors. Additional investigation and photography under UV light to reveal details of the bones not easily seen under normal lighting regimes was completed.
This taxon heralds from a newly explored locality that is older than the classic Solnhofen beds. While similar to Rhamphorhynchus, the new taxon differs in the number of teeth, shape of the humerus and femur, and limb proportions. Unlike other derived non-pterodacytyloids, Bellubrunnus lacks elongate chevrons and zygapophyses in the tail, and unlike all other known pterosaurs, the wingtips are curved anteriorly, potentially giving it a unique flight profile.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Core Ideas
Manure N transformation was modeled with different soil pore connectivities to tile drains.
Macropores facilitated NH4+ oxidation reaction products deeper in the profile.
Nitrate losses to ...tile were best predicted by models using pores connected to tile drains.
Macropores can be important conduits for surface‐derived nutrients to reach subsurface receptors. Accordingly, nutrient reactive transport processes in macroporous soils need to be well understood. In this study, steady‐state two‐dimensional reactive transport simulations with MIN3P‐THCm (version 1.0.519.0) were used to elucidate how soil macropore connectivity to tile drains can influence N transformations following liquid swine manure (LSM) applications to soil. Four different soil scenarios were considered: homogeneous sand, homogeneous clay loam, and clay loam with discrete macropores connected to or disconnected from the bottom boundary used to represent tile drain outflow. In relation to the homogeneous soils, macropores, overall, facilitated chemical diffusion into the adjacent soil matrix along their length and broadly augmented O2 ingress into the soil profile. These processes combined to critically control the spatial distribution of NH4+ oxidation reaction products. When used in transient simulation mode with field data observed at experimental tile‐drained plots that received LSM application, the model showed that simulated nitrate mass losses to tile are considerably higher and most realistic under the connected macropore scenario compared with the homogeneous or disconnected macropore scenarios.
Cell-free biomanufacturing Bundy, Bradley C; Hunt, J Porter; Jewett, Michael C ...
Current opinion in chemical engineering,
12/2018, Letnik:
22, Številka:
C
Journal Article
Odprti dostop
Since its early development and use to decipher the genetic code, in vitro or ‘cell-free’ systems have been used as an important research tool to understand biochemical mechanisms and metabolic ...pathways. More recently, due to important engineering advances the technology is rapidly becoming a biomanufacturing platform for protein therapeutics, vaccines, enzyme biocatalysts, fuels, and commodity chemicals. Here we report recent applications and advances in the cell-free biomanufacturing field and the potential of this emerging approach.
The use of cell‐free systems to produce recombinant proteins has grown rapidly over the past decade. In particular, cell‐free protein synthesis (CFPS) systems based on mammalian cells provide ...alternative methods for the production of many proteins, including those that contain disulfide bonds, glycosylation, and complex structures such as monoclonal antibodies. In the present study, we show robust production of turbo green fluorescent protein (tGFP) and streptokinase in a cell‐free system using instrumented mini‐bioreactors for highly reproducible protein production. We achieved recombinant protein production (∼600 μg/ml of tGFP and 500 μg/ml streptokinase) in 2.5 hr of expression time, comparable to previously reported yields for cell‐free protein expression. Also, we demonstrate the use of two different affinity tags for product capture and compare those to a tag‐free self‐cleaving intein capture technology. The intein purification method provided a product recovery of 86%, compared with 52% for conventionally tagged proteins, while resulting in a 30% increase in total units of activity of purified recombinant streptokinase compared with conventionally tagged proteins. These promising beneficial features combined with the intein technology makes feasible the development of dose‐level production of therapeutic proteins at the point‐of‐care.
In the present study, a cell‐free protein synthesis was explored to produce recombinant streptokinase using CHO lysate. Two different affinity tags were used for protein capture and compared to a tag‐free self‐cleaving intein capture technology. The intein purification method provided greater product recovery and activity compared with conventionally tagged proteins. Cell‐free protein synthesis combined with the intein technology makes feasible the rapid production of dose‐level production of therapeutic proteins at the point‐of‐care.
The West Siberian Lowland (WSL) contains the world's most extensive peatlands and a substantial fraction of the global terrestrial carbon pool. Despite its recognition as a carbon reservoir of great ...significance, the extent, thickness, and carbon content of WSL peatlands have not been analyzed in detail. This paper compiles a wide array of data into a geographic information system (GIS) to create a high‐resolution, spatially explicit digital inventory of all WSL peatlands and their associated physical properties. Detailed measurements for nearly 10,000 individual peatlands (patches) are based on compilation of previously unpublished Russian field and ancillary map data, satellite imagery, previously published depth measurements, and our own field depth and core measurements taken throughout the region during field campaigns in 1999, 2000, and 2001. At the patch level, carbon storage is estimated as the product of peatland area, depth, and carbon content. Estimates of peatland area are validated from RESURS‐01 satellite images, and the quality of the Russian peatland depth and carbon content data is independently confirmed by laboratory analysis of core samples. Through GIS‐based spatial analysis of the peat areal extent, depth, and carbon content data, we conservatively estimate the total area of WSL peatlands at 592,440 km2, the total peat mass at 147.82 Pg, and the total carbon pool at 70.21 Pg C. Our analysis concludes that WSL peatlands are more extensive and represent a substantially larger carbon pool than previously thought: Previous studies report 9,440–273,440 km2 less peatland area and 15.11–30.19 Pg less carbon than found in this analysis. The complete digital database is freely available for scientific use at http://arcss.colorado.edu/data/arcss131.html.
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