scholarly journals The DOE Systems Biology Knowledgebase (KBase)

2016 ◽  
Author(s):  
Adam P Arkin ◽  
Rick L Stevens ◽  
Robert W Cottingham ◽  
Sergei Maslov ◽  
Christopher S Henry ◽  
...  
Keyword(s):  
Systems Biology ◽  
Open Source Software ◽  
Large Scale ◽  
Community Dynamics ◽  
Department Of Energy ◽  
Small Scale ◽  
Grand Challenge ◽  
Web Browser ◽  
Data Platform ◽  
Computational Resources

AbstractThe U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

scholarly journals Rapid evolution by spontaneous mutation increases genetic diversity facilitating plant population survival

2018 ◽  
Author(s):  
Henning Nottebrock ◽  
Mao-Lun Weng ◽  
Matthew T Rutter ◽  
Charles B. Fenster
Keyword(s):  
Large Scale ◽  
Community Dynamics ◽  
Spontaneous Mutation ◽  
Rapid Evolution ◽  
Potential Effect ◽  
Small Scale ◽  
Negative Effects ◽  
Population Survival ◽  
Population And Community Dynamics ◽  
The Impact

Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on spatial interactions to better understand the potential effect of niche evolution through mutations on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale, survival is enhanced but reproduction is decreased when a genotype is surrounded by different genotypes. At large-scale, seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. Mutations may provide a mechanism for plants to quickly evolve niches and may drive competition, facilitation and selection with profound consequences for future population and community dynamics.

Efficient Computational Model for Non-Axisymmetric Flow and Heat Transfer in Rotating Cavity

2008 ◽  
Author(s):  
L. He
Keyword(s):  
Large Scale ◽  
Axisymmetric Flow ◽  
Small Scale ◽  
Vortex Pairs ◽  
Spectral Technique ◽  
Flow And Heat Transfer ◽  
Large Length ◽  
Computational Resources ◽  
Fourier Harmonics ◽  
Computational Predictions

Existence of large scale unsteady flow structures manifested in contra-rotating vortex pairs has been previously identified in rotor disc cavities. The non-axisymmetric nature with a unknown number of vortices presents a computational challenge as a full 360° circumferential domain will be needed, requiring significant computational resources. A novel circumferential spatial Fourier spectral technique is adopted in the present work to facilitate efficient computational predictions of the non-axisymmetric flows. Given that the flow non-uniformities in the circumferential direction are of large length scales, only a few circumferential Fourier harmonics would be needed, resulting in a drastic reduction in number of circumferential mesh points to be required. The modeling formulations and implementation aspects will be described. Computational examples will be presented to demonstrate the validity and effectiveness of the present modeling approach. The computational results show that the non-axisymmetric flow patterns in terms of the number of vortex pairs are sensitive to small scale external disturbances. It is also indicated that the occurrence of a non-axisymmetric flow might be captured by the present Fourier solution with even one harmonic.

Efficient Computational Model for Nonaxisymmetric Flow and Heat Transfer in Rotating Cavity

2010 ◽  
Vol 133 (2) ◽  
Author(s):  
L. He
Keyword(s):  
Large Scale ◽  
Small Scale ◽  
Vortex Pairs ◽  
Spectral Technique ◽  
Flow And Heat Transfer ◽  
Large Length ◽  
Rotor Disk ◽  
Computational Resources ◽  
Fourier Harmonics ◽  
Computational Predictions

Existence of large scale unsteady flow structures manifested in contrarotating vortex pairs has been previously identified in rotor disk cavities. The nonaxisymmetric nature with an unknown number of vortices presents a computational challenge, as a full 360 deg circumferential domain will be needed, requiring significant computational resources. A novel circumferential spatial Fourier spectral technique is adopted in the present work to facilitate efficient computational predictions of the nonaxisymmetric flows. Given that the flow nonuniformities in the circumferential direction are of large length scales, only a few circumferential Fourier harmonics would be needed, resulting in a drastic reduction in number of circumferential mesh points to be required. The modeling formulations and implementation aspects will be described. Computational examples will be presented to demonstrate the validity and effectiveness of the present modeling approach. The computational results show that the nonaxisymmetric flow patterns, in terms of the number of vortex pairs, are sensitive to small scale external disturbances. It is also indicated that the occurrence of a nonaxisymmetric flow might be captured by the present Fourier solution with even one harmonic.

Diagnostic Comparison of Meteorological Analyses during the 2002 Antarctic Winter

2005 ◽  
Vol 133 (5) ◽  
pp. 1261-1278 ◽  
Author(s):  
Gloria L. Manney ◽  
Douglas R. Allen ◽  
Kirstin Krüger ◽  
Barbara Naujokat ◽  
Michelle L. Santee ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Large Scale ◽  
Meteorological Data ◽  
Polar Vortex ◽  
Department Of Energy ◽  
Observation System ◽  
Small Scale ◽  
Stratospheric Temperature ◽  
Transport Barriers ◽  
Environmental Prediction

Abstract Several meteorological datasets, including U.K. Met Office (MetO), European Centre for Medium-Range Weather Forecasts (ECMWF), National Centers for Environmental Prediction (NCEP), and NASA’s Goddard Earth Observation System (GEOS-4) analyses, are being used in studies of the 2002 Southern Hemisphere (SH) stratospheric winter and Antarctic major warming. Diagnostics are compared to assess how these studies may be affected by the meteorological data used. While the overall structure and evolution of temperatures, winds, and wave diagnostics in the different analyses provide a consistent picture of the large-scale dynamics of the SH 2002 winter, several significant differences may affect detailed studies. The NCEP–NCAR reanalysis (REAN) and NCEP–Department of Energy (DOE) reanalysis-2 (REAN-2) datasets are not recommended for detailed studies, especially those related to polar processing, because of lower-stratospheric temperature biases that result in underestimates of polar processing potential, and because their winds and wave diagnostics show increasing differences from other analyses between ∼30 and 10 hPa (their top level). Southern Hemisphere polar stratospheric temperatures in the ECMWF 40-Yr Re-analysis (ERA-40) show unrealistic vertical structure, so this long-term reanalysis is also unsuited for quantitative studies. The NCEP/Climate Prediction Center (CPC) objective analyses give an inferior representation of the upper-stratospheric vortex. Polar vortex transport barriers are similar in all analyses, but there is large variation in the amount, patterns, and timing of mixing, even among the operational assimilated datasets (ECMWF, MetO, and GEOS-4). The higher-resolution GEOS-4 and ECMWF assimilations provide significantly better representation of filamentation and small-scale structure than the other analyses, even when fields gridded at reduced resolution are studied. The choice of which analysis to use is most critical for detailed transport studies (including polar process modeling) and studies involving synoptic evolution in the upper stratosphere. The operational assimilated datasets are better suited for most applications than the NCEP/CPC objective analyses and the reanalysis datasets (REAN/REAN-2 and ERA-40).

Survey of trematodes in intertidal snails from Patagonia, Argentina: new larval forms and diversity assessment

2018 ◽  
Vol 93 (3) ◽  
pp. 342-351 ◽  
Author(s):  
C. Gilardoni ◽  
G. Di Giorgio ◽  
E. Bagnato ◽  
F. Cremonte
Keyword(s):  
Large Scale ◽  
Community Dynamics ◽  
Life Cycles ◽  
Trematode Species ◽  
Small Scale ◽  
Intermediate Hosts ◽  
Scale Factors ◽  
Diversity Assessment ◽  
Southern Patagonia ◽  
Population And Community Dynamics

AbstractLarval trematodes are the main parasites of snails, and they play a crucial role because they usually castrate their snail hosts and can thus alter their population and community dynamics. This study involved a survey of seven gastropod species (Crepipatella dilatata,Fissurella radiosa,Nacella magellanica,Pareuthria fuscata,Siphonaria lessonii, S. lateralisandTrophon geversianus) parasitized by 12 trematode species (one hemiurid, one gymnophallid, two lepocreadiids, two microphallids, one notocotylid, two renicolids, one philophtalmid, one schistosomatid and one zoogonid) from southern Patagonia (47°S, 65°W), Argentina. OnlyF. radiosawas free of parasites. The study included the description of five new larvae, based on morphological and molecular information, and a comparison of the parasite diversity with that of a northern locality (42°S, 64°W), characterized by a lower mollusc diversity. Species richness and diversity of parasites were higher in the southern site. This suggests a correlation between the level of parasitism and the diversity of molluscs (first intermediate hosts), which is higher at the high-latitude site and seems to attract shorebirds, which disperse the digenean eggs and facilitate the completion of their life cycles. These results support the notion that parasitism is influenced by large-scale factors such as biogeographical patterns, and small-scale factors such as diversity or abundance of intermediate and definitive hosts.

scholarly journals Intraspecific Competitive Interactions Rapidly Evolve Via Spontaneous Mutations

2022 ◽  
Author(s):  
Henning Nottebrock ◽  
Mao-Lun Weng ◽  
Matthew T. Rutter ◽  
Charles B. Fenster
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Community Dynamics ◽  
Seed Set ◽  
Small Scale ◽  
Negative Effects ◽  
Plant Seed ◽  
Fifth Generation ◽  
Population And Community Dynamics ◽  
The Impact

Abstract Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on intraspecific spatial interactions to better understand mechanisms underlying the maintenance of genetic variation and the potential effects of these evolved interactions on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale (within 80 cm of the focal plant), survival is enhanced but seed-set is decreased when a genotype is surrounded by different genotypes. At large-scale (within 200 cm of the focal plant), seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. The direction of the interactions among MA lines suggests that at small scale these interactions may contribute to the maintenance of genetic variation and at large scale contribute to the survival of the population. This may suggest, that, mutations potentially have immediate effects on population and community dynamics by influencing the outcome of competitive and faciliatory interactions among conspecifics.

scholarly journals Opportunities from low-resolution modelling of river morphology in remote parts of the world

2014 ◽  
Vol 2 (1) ◽  
pp. 9-19 ◽  
Author(s):  
M. Nones ◽  
M. Guerrero ◽  
P. Ronco
Keyword(s):  
Cross Sections ◽  
Large Scale ◽  
Initial Conditions ◽  
Large Rivers ◽  
Small Scale ◽  
First Case ◽  
The World ◽  
High Level ◽  
Computational Resources

Abstract. River morphodynamics are the result of a variety of processes, ranging from the typical small-scale of fluid mechanics (e.g. flow turbulence dissipation) to the large-scale of landscape evolution (e.g. fan deposition). However, problems inherent in the long-term modelling of large rivers derive from limited computational resources and the high level of process detail (i.e. spatial and temporal resolution). These modelling results depend on processes parameterization and calibrations based on detailed field data (e.g. initial morphology). Thus, for these cases, simplified tools are attractive. In this paper, a simplified 1-D approach is presented that is suited for modelling very large rivers. A synthetic description of the variations of cross-sections shapes is implemented on the basis of satellite images, typically also available for remote parts of the world. The model's flexibility is highlighted here by presenting two applications. In the first case, the model is used for analysing the long-term evolution of the lower Zambezi River (Africa) as it relates to the construction of two reservoirs for hydropower exploitation. In the second case, the same model is applied to study the evolution of the middle and lower Paraná River (Argentina), particularly in the context of climate variability. In both cases, having only basic data for boundary and initial conditions, the 1-D model provides results that are in agreement with past studies and therefore shows potential to be used to assist sediment management at the watershed scale or at boundaries of more detailed models.

Small-Scale Science to Large-Scale Profession

2000 ◽  
Vol 45 (4) ◽  
pp. 396-398
Author(s):  
Roger Smith
Keyword(s):  
Large Scale ◽  
Small Scale

Development of Physics Learning Module Based on Guided Inquiry with Light Wave Material in Class XI of Senior High School

2020 ◽  
Vol 1 (1) ◽  
pp. 1-10
Author(s):  
Evi Rahmawati ◽  
Irnin Agustina Dwi Astuti ◽  
N Nurhayati
Keyword(s):  
Large Scale ◽  
Learning Strategy ◽  
Student Response ◽  
Average Score ◽  
Small Scale ◽  
Design Development ◽  
Teacher Response ◽  
Student Responses ◽  
Analysis Design ◽  
Scientific Skills

IPA Integrated is a place for students to study themselves and the surrounding environment applied in daily life. Integrated IPA Learning provides a direct experience to students through the use and development of scientific skills and attitudes. The importance of integrated IPA requires to pack learning well, integrated IPA integration with the preparation of modules combined with learning strategy can maximize the learning process in school. In SMP 209 Jakarta, the value of the integrated IPA is obtained from 34 students there are 10 students completed and 24 students are not complete because they get the value below the KKM of 68. This research is a development study with the development model of ADDIE (Analysis, Design, Development, Implementation, and Evaluation). The use of KPS-based integrated IPA modules (Science Process sSkills) on the theme of rainbow phenomenon obtained by media expert validation results with an average score of 84.38%, average material expert 82.18%, average linguist 75.37%. So the average of all aspects obtained by 80.55% is worth using and tested to students. The results of the teacher response obtained 88.69% value with excellent criteria. Student responses on a small scale acquired an average score of 85.19% with highly agreed criteria and on the large-scale student response gained a yield of 86.44% with very agreed criteria. So the module can be concluded receiving a good response by the teacher and students.

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