scholarly journals The BioCyc collection of microbial genomes and metabolic pathways

2017 ◽  
Vol 20 (4) ◽  
pp. 1085-1093 ◽  
Author(s):  
Peter D Karp ◽  
Richard Billington ◽  
Ron Caspi ◽  
Carol A Fulcher ◽  
Mario Latendresse ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Metabolic Pathways ◽  
Biomedical Literature ◽  
Analysis Software ◽  
New Developments ◽  
Microbial Genomes ◽  
Additional Information ◽  
Alignment Tool ◽  
Extensive Range ◽  
Types Of Information

Abstract BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance.

scholarly journals VirusDIP: Virus Data Integration Platform

2020 ◽  
Author(s):  
Lina Wang ◽  
Fengzhen Chen ◽  
Xueqin Guo ◽  
Lijin You ◽  
Xiaoxia Yang ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Sequence Data ◽  
Data Retrieval ◽  
Viral Sequence ◽  
Origin And Evolution ◽  
Alignment Tool ◽  
Public Data ◽  
Virus Research ◽  
Global Initiative ◽  
Tree Building

AbstractMotivationThe Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created.ResultsTo facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide.Availabilityhttps://db.cngb.org/virus/[email protected]

scholarly journals Pathway swapping: Toward modular engineering of essential cellular processes

2016 ◽  
Vol 113 (52) ◽  
pp. 15060-15065 ◽  
Author(s):  
Niels G. A. Kuijpers ◽  
Daniel Solis-Escalante ◽  
Marijke A. H. Luttik ◽  
Markus M. M. Bisschops ◽  
Francine J. Boonekamp ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Pathways ◽  
Applied Research ◽  
Central Metabolism ◽  
Microbial Genomes ◽  
Cellular Processes ◽  
Recent Developments ◽  
One Step ◽  
Saccharomyces Kudriavzevii

Recent developments in synthetic biology enable one-step implementation of entire metabolic pathways in industrial microorganisms. A similarly radical remodelling of central metabolism could greatly accelerate fundamental and applied research, but is impeded by the mosaic organization of microbial genomes. To eliminate this limitation, we propose and explore the concept of “pathway swapping,” using yeast glycolysis as the experimental model. Construction of a “single-locus glycolysis” Saccharomyces cerevisiae platform enabled quick and easy replacement of this yeast’s entire complement of 26 glycolytic isoenzymes by any alternative, functional glycolytic pathway configuration. The potential of this approach was demonstrated by the construction and characterization of S. cerevisiae strains whose growth depended on two nonnative glycolytic pathways: a complete glycolysis from the related yeast Saccharomyces kudriavzevii and a mosaic glycolysis consisting of yeast and human enzymes. This work demonstrates the feasibility and potential of modular, combinatorial approaches to engineering and analysis of core cellular processes.

How much is a calorie worth? A study of willingness to pay for calorie labels in restaurant menus

2019 ◽  
pp. 1-24
Author(s):  
SANA RAFIQ
Keyword(s):  
Willingness To Pay ◽  
Well Being ◽  
Economic Benefits ◽  
Individual Level ◽  
Additional Information ◽  
Health Related ◽  
The Individual ◽  
Types Of Information ◽  
Caloric Consumption ◽  
The Impact

AbstractWe asked individuals about their willingness to pay (WTP) either: (1) for a mandate requiring restaurants to post calorie information on their menus; or (2) to avoid such a mandate. On average, more people were in in favor of the mandate and were willing to pay four times more than those who were against it, thereby leading to a Kaldor–Hicks improvement from this policy. To ensure robustness, we tested the impact of providing three types of information during individuals’ WTP determinations: (1) visual examples of the proposed calorie labels; (2) data on their effectiveness at the individual level; and (3) data on their wider social and economic benefits. For those in favor, providing a simple visual of the label had no impact on WTP. Data on the individual effectiveness of the labels increased the WTP, while evidence on broader obesity reduction and economic benefits reduced it. For opponents, WTP did not change with provision of additional information except when provided with information on social and economic benefits. Under this condition, the opponents increased their WTP 12-fold to avoid a mandate of this policy. Finally, we measured individual well-being under this policy and found directionally similar results, confirming a net improvement in aggregate welfare. Our results suggest that messaging that focuses on private benefits (providing calorie information so that individuals can effectively choose to reduce excessive caloric consumption) rather than wider public benefits (reduction in overall health-related costs and obesity) is more likely to be effective.

North China Plain

2017 ◽  
Author(s):  
Laurel Bossen ◽  
Hill Gates
Keyword(s):  
Rural China ◽  
Local Environment ◽  
Northern China ◽  
Early Research ◽  
Hebei Province ◽  
New Developments ◽  
Cotton Industry ◽  
Additional Information ◽  
Starting Point ◽  
Economic Background

This chapter demonstrates how pervasive footbinding was among the mothers and grandmothers of women we interviewed in northern China. It begins by outlining political and economic background to the region and the development of the preindustrial cotton industry. Hebei province, surrounding Beijing, is the starting point. Heavily influenced by political changes and new developments in transportation and trade, Ding County, was the site of a landmark study of rural China in the 1920s and 1930s. Complementing the early research with new village material provides different perspectives on Ding County's decline in footbinding. Research in villages in Shandong, Henan, and Anhui Provinces provides additional information on the interplay of local environment, trade, girls’ hand labor, the pattern of footbinding and the pace of its decline.

scholarly journals New developments in engineering plant metabolic pathways

2016 ◽  
Vol 42 ◽  
pp. 126-132 ◽  
Author(s):  
Evangelos C Tatsis ◽  
Sarah E O’Connor
Keyword(s):  
Metabolic Pathways ◽  
Engineering Plant ◽  
New Developments

scholarly journals PMBD: a Comprehensive Plastics Microbial Biodegradation Database

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Zhiqiang Gan ◽  
Houjin Zhang
Keyword(s):  
Sequence Alignment ◽  
Prediction Tool ◽  
Literature Searching ◽  
Environmentally Conscious ◽  
Uniprot Database ◽  
Online Resource ◽  
Alignment Tool ◽  
Microbial Biodegradation ◽  
Tremendous Amount ◽  
Natural Way

Abstract Since the invention over a hundred years ago, plastics have been used in many applications, and they are involved in every aspect of our lives. The extensive usage of plastics results in a tremendous amount of waste, which has become a severe burden on the environment. Several degradation approaches exist in nature to cope with ever-increasing plastic waste. Among these approaches, biodegradation by microorganisms has emerged as a natural way, which is favored by many environmentally conscious societies. To facilitate the study on biodegradation of plastics, we developed an online resource, Plastics Microbial Biodegradation Database (PMBD), to gather and present the information about microbial biodegradation of plastics. In this database, 949 microorganisms–plastics relationships and 79 genes involved in the biodegradation of plastics were manually collected and confirmed through literature searching. In addition, more than 8000 automatically annotated enzyme sequences, which were predicted to be involved in the plastics biodegradation, were extracted from the TrEMBL section of the UniProt database. The PMBD database is presented with a website at http://pmbd.genome-mining.cn/home. Data may be accessed through browsing or searching. Also included on the website are a sequence alignment tool and a function prediction tool.

Effect of Occupational Prestige and Attitude Similarity on Attraction as a Function of Assumed Similarity of Attitude

1968 ◽  
Vol 23 (3_suppl) ◽  
pp. 1167-1172 ◽  
Author(s):  
Michael Bond ◽  
Donn Byrne ◽  
Michael J. Diamond
Keyword(s):  
Positive Function ◽  
Occupational Prestige ◽  
Attitude Similarity ◽  
Additional Information ◽  
Occupational Information ◽  
Assumed Similarity ◽  
Types Of Information ◽  
The Stranger ◽  
The Prestige

Previous research has shown that the effect of attitudes on attraction is independent of the prestige or status of the stranger expressing the attitudes. It was hypothesized that in the absence of additional information, attraction toward a stranger is a positive function of his occupational prestige and that attraction is a positive function of assumed attitudinal similarity between stranger and S. Ss were 139 Stanford students who were given either occupational information, attitudinal information, or both types of information about a stranger. It was found that either occupational information alone ( p < .02) or attitudinal information alone ( p < .001) influences attraction. When the two types of information are combined, as in earlier research, Ss respond only to attitude similarity ( p < .001). There was support for the proposed relationship between attraction and assumed similarity ( p < .01), but variations across conditions suggest caution in interpreting this finding.

scholarly journals Predicting Novel Metabolic Pathways through Subgraph Mining

2017 ◽  
Author(s):  
Aravind Sankar ◽  
Sayan Ranu ◽  
Karthik Raman
Keyword(s):  
Metabolic Pathways ◽  
Reliable Method ◽  
Edit Distance ◽  
Directed Search ◽  
Reaction Centre ◽  
Additional Information ◽  
Chemical Structures ◽  
Subgraph Mining ◽  
Reaction Rule ◽  
Atom Mapping

AbstractThe ability to predict pathways for biosynthesis of metabolites is very important in metabolic engineering. It is possible to mine the repertoire of biochemical transformations from reaction databases, and apply the knowledge to predict reactions to synthesize new molecules. However, this usually involves a careful understanding of the mechanism and the knowledge of the exact bonds being created and broken. There is clearly a need for a method to rapidly predict reactions for synthesizing new molecules, which relies only on the structures of the molecules, without demanding additional information such as thermodynamics or hand-curated information such as atom-atom mapping, which are often hard to obtain accurately.We here describe a robust method based on subgraph mining, to predict a series of biochemical transformations, which can convert between two (even previously unseen) molecules. We first describe a reliable method based on subgraph edit distance to map reactants and products, using only their chemical structures. Having mapped reactants and products, we identify the reaction centre and its neighbourhood, the reaction signature, and store this in a reaction rule network. This novel representation enables us to rapidly predict pathways, even between previously unseen molecules. We also propose a heuristic that predominantly recovers natural biosynthetic pathways from amongst hundreds of possible alternatives, through a directed search of the reaction rule network, enabling us to provide a reliable ranking of the different pathways. Our approach scales well, even to databases with > 100,000 reactions. A Java-based implementation of our algorithms is available at https://github.com/RamanLab/ReactionMinerCCS CONCEPTS•Information systems →Data mining; •Applied computing →Bioinformatics;

Public Perception Spatial Data From the PPGIS Jaguarão Experiment

2019 ◽  
pp. 177-198
Author(s):  
Geisa Bugs ◽  
Marketta Kyttä
Keyword(s):  
Urban Space ◽  
Spatial Data ◽  
Public Perception ◽  
The Public ◽  
Additional Information ◽  
Information Layer ◽  
Other Information ◽  
Types Of Information ◽  
Socioeconomic Data ◽  
Participatory Method

This chapter addresses PPGIS (Public Participation Geographic Information Systems), a participatory method through which the public can produce maps and spatial data that represent their perceptions of the urban space in question. Specifically, it analyzes the data collected from an experiment in Jaguarão, Brazil. The data represents the perceptions of a small group of inhabitants about the problems and potential of the city's urban area. The procedures include an exploratory analysis and data visualization in the form of maps that allow describing a variable's distribution and identifying patterns. Moreover, for some issues, the authors cross the perception collected data with infrastructure data, socioeconomic data, and cadastral data to study possible associations among these different types of information layers. The results show that public perception, collected through PPGIS, forms an additional information layer that could be analyzed together with other information layers commonly used in urban planning, and thus to be taken into account for designing better cities.

Qualitative data analysis software: The state of the art

KWALON ◽  
2016 ◽  
Vol 21 (1) ◽  
Author(s):  
Susanne Friese
Keyword(s):  
Data Analysis ◽  
Qualitative Data ◽  
Critical Appraisal ◽  
State Of The Art ◽  
The State ◽  
Data Driven ◽  
Analysis Software ◽  
Qualitative Data Analysis ◽  
New Developments ◽  
Qualitative Data Analysis Software

Summary The aim of this paper is to provide an overview of the ‘state of the art of QDA or CAQDAS software. The author uses Kahneman’s ideas about slow and fast thinking as a framework. Slow thinking in the context of CAQDAS is related to researcher driven analysis and fast thinking to tool- and data driven analysis. The paper is divided into two parts. In the first part, the author describes trends and new developments and in the second part, she offers a critical appraisal.

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