scholarly journals Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data

2021 ◽  
Vol 9 (4) ◽  
pp. 840
Author(s):  
Joao Pedro Saraiva ◽  
Anja Worrich ◽  
Canan Karakoç ◽  
Rene Kallies ◽  
Antonis Chatzinotas ◽  
...  
Keyword(s):  
Species Interactions ◽  
Imaging Techniques ◽  
Research Question ◽  
Search Space ◽  
Ecosystem Processes ◽  
Microbial Interactions ◽  
Complex Nature ◽  
Interspecies Interactions ◽  
Genetic Potential ◽  
Starting Point

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

scholarly journals Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data

2021 ◽  
Author(s):  
João Pedro Saraiva ◽  
Anja Worrich ◽  
Canan Karakoç ◽  
Rene Kallies ◽  
Antonis Chatzinotas ◽  
...  
Keyword(s):  
Species Interactions ◽  
Imaging Techniques ◽  
Research Question ◽  
Building Blocks ◽  
Search Space ◽  
Ecosystem Processes ◽  
Microbial Interactions ◽  
Complex Nature ◽  
Interspecies Interactions ◽  
Genetic Potential

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used to define the building blocks to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

scholarly journals OrtSuite – from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Author(s):  
João Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

Abstract The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96 % of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

OrtSuite – a flexible pipeline for annotation of ecosystem processes and prediction of putative microbial interactions

2020 ◽  
Author(s):  
João Pedro Saraiva ◽  
Marta Gomes ◽  
René Kallies ◽  
Carsten Vogt ◽  
Antonis Chatzinotas ◽  
...  
Keyword(s):  
Functional Annotation ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Microbial Community Composition ◽  
Ecosystem Processes ◽  
Microbial Interactions ◽  
Interspecies Interactions ◽  
Sequencing Data ◽  
Computer Clusters ◽  
Identity Threshold

Abstract Background: The exponential increase in high-throughput sequencing data and the development of computational sciences and bioinformatics pipelines has advanced our understanding of microbial community composition and distribution in complex ecosystems. Despite these advances, the identification of microbial interactions from genomic data remains a major bottleneck. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content. Results: OrtSuite combines ortholog clustering strategies with genome annotation based on a user-defined set of functions allowing for hypothesis-driven data analysis. OrtSuit allows users to install and run all workflow components and analyze the generated outputs using a simple pipeline consisting of 23 bash commands and one R command. Annotation is based on a two-stage process. First, only a subset of sequences from each ortholog cluster are aligned to all sequences in the Ortholog-Reaction Association database (ORAdb). Next, all sequences from clusters that meet a user-defined identity threshold are aligned to all sequence sets in ORAdb to which they had a hit. This approach results in a decrease in time needed for functional annotation. Further, OrtSuit identifies putative interspecies interactions based on their individual genomic content based on constrains given by the users. Additional control is afforded to the user at several stages of the workflow: 1) The construction of ORAdb only needs to be performed once for each specific process also allowing manual curation; 2) The identity and sequence similarity thresholds used during the annotation stage can be adjusted; and 3) Constraints related to pathway reaction composition and known species contributions to ecosystem processes can be defined. Conclusions: OrtSuit is an easy to use workflow that allows for rapid functional annotation based on a user curated database. Further, this novel workflow allows the identification of interspecies interactions through user-defined constrains. Due to its low computational demands, for small datasets (e.g. maximum 100 genomes) OrtSuit can run on a personal computer. For larger datasets (> 100 genomes), we suggest the use of computer clusters. OrtSuit is an open-source software available at https://github.com/mdsufz/OrtSuit .

scholarly journals OrtSuite – from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Author(s):  
Joao Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Vinicios Fleming Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96 % of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. Identification of putative synergistic species interactions was evaluated using the sequenced genomes of an independent study which had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy to use workflow that allows for rapid functional annotation based on a user curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

scholarly journals OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Vol 4 (12) ◽  
pp. e202101167
Author(s):  
João Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

scholarly journals Living lab on sharing and circular economy: The case of Turin

2021 ◽  
Vol 27 (1) ◽  
pp. 146045822098727
Author(s):  
Federico Cuomo ◽  
Nadia Lambiase ◽  
Antonio Castagna
Keyword(s):  
Circular Economy ◽  
Common Ground ◽  
Swot Analysis ◽  
Research Question ◽  
Environmental Benefits ◽  
Production Cycle ◽  
Living Lab ◽  
Starting Point ◽  
Living Labs ◽  
Past Experiences

Cities with their innovative capacity are key places to address critical climate, environmental and health challenges. Urban experimentations, such as Living Labs, can represent a starting point to reintroduce resources into the production cycle and reduce environmental impacts, embracing the paradigm of the circular economy (CE). According to recent studies, Living Labs at a city scale could generate significant environmental benefits, improvements in quality of life and positive impacts on citizens’ health.1 This paper aims at presenting the case of the Torino Living Lab on Sharing and Circular Economy (LLSC) to point out possible future scenarios of urban sustainable policies. The case study is analysed in five sections: (1) the description of the new permanent laboratory proposed by the City of Turin; (2) the past experiences of Living Labs in Turin; (3) the birth of LLSC and the involvement strategy; (4) the introduction of the eight admitted experimentations. In the light of the results collected, the last paragraph (5) came up with the Strengths, Weaknesses, Opportunities, Treaths (SWOT) analysis in the LLSC. Eventually, it deals with the research question by offering a common ground for global and local policies focused on sustainability and CE.

scholarly journals Consumer Neuroscience Techniques in Advertising Research: A Bibliometric Citation Analysis

2021 ◽  
Vol 13 (3) ◽  
pp. 1589
Author(s):  
Juan Sánchez-Fernández ◽  
Luis-Alberto Casado-Aranda ◽  
Ana-Belén Bastidas-Manzano
Keyword(s):  
Self Report ◽  
Future Research ◽  
Complex Nature ◽  
Clear Understanding ◽  
Continuous Growth ◽  
Main Research ◽  
Consumer Neuroscience ◽  
Starting Point ◽  
Wide Range ◽  
Performance Analysis Tools

The limitations of self-report techniques (i.e., questionnaires or surveys) in measuring consumer response to advertising stimuli have necessitated more objective and accurate tools from the fields of neuroscience and psychology for the study of consumer behavior, resulting in the creation of consumer neuroscience. This recent marketing sub-field stems from a wide range of disciplines and applies multiple types of techniques to diverse advertising subdomains (e.g., advertising constructs, media elements, or prediction strategies). Due to its complex nature and continuous growth, this area of research calls for a clear understanding of its evolution, current scope, and potential domains in the field of advertising. Thus, this current research is among the first to apply a bibliometric approach to clarify the main research streams analyzing advertising persuasion using neuroimaging. Particularly, this paper combines a comprehensive review with performance analysis tools of 203 papers published between 1986 and 2019 in outlets indexed by the ISI Web of Science database. Our findings describe the research tools, journals, and themes that are worth considering in future research. The current study also provides an agenda for future research and therefore constitutes a starting point for advertising academics and professionals intending to use neuroimaging techniques.

scholarly journals Implications of Lesson Study for Tertiary-Level EFL Teachers’ Professional Development: A Case Study From Turkey

SAGE Open ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 215824402110237
Author(s):  
İlknur Bayram ◽  
Fatma Bıkmaz
Keyword(s):  
Professional Development ◽  
Lesson Study ◽  
English Language ◽  
Research Question ◽  
Teaching Style ◽  
Language Teachers ◽  
Student Thinking ◽  
Pedagogical Content ◽  
Starting Point

This qualitative case study carried out at a Turkish university with four English language teachers aims to explore what teachers experience in the planning, implementation, analysis, and reporting phases of the lessons study process and what the implications of lesson study for teacher professional development can be. Data in this four-month study were gathered through observations, interviews, whole group discussions, and reflective reports. Findings revealed that lesson study had potential challenges and benefits for the professional development of teachers. The model poses challenges in finding a topic and research question, determining the lesson design and teaching style, making student thinking observable and analyzing qualitative data. On the other hand, it benefited teachers in terms of increasing their pedagogical content knowledge, reflectivity, research skills, collaboration, and collegiality. This study suggests that lesson study might be a good starting point for institutions wishing to adopt a more teacher-led, inquiry-driven and collaborative perspective for professional development.

Selected issues related to the use of firearms for unlawful killing of animals

2018 ◽  
Vol 301 ◽  
pp. 53-59
Author(s):  
Daniel Markiewicz ◽  
◽  
Bartłomiej J. Bartyzel ◽  
Michał Borusiński ◽  
Grzegorz Bogiel ◽  
...  
Keyword(s):  
Law Enforcement ◽  
Imaging Techniques ◽  
Gunshot Wounds ◽  
Legal Regulation ◽  
Post Mortem ◽  
Large Mammals ◽  
Law Enforcement Agencies ◽  
Scientific Institutions ◽  
Starting Point ◽  
Penal Sanctions

The issue of post-mortem examination of animals, whose death occurred as a result of suffered gunshot wounds, is very rarely discussed in literature, most often on the occasion of researching into and describing other problems. This article presents an attempt to bring together the achievements of veterinary forensics in this area. As a starting point, the current legal regulation was adopted, pointing to penal sanctions resulting from the illegal use of weapons in relation to animals. Subsequently, the possibilities of using modern imaging techniques in post-mortem examinations carried out by veterinarians at the request of law enforcement agencies were presented. The scientific reports discussed herein have been supplemented by examples of sectional examinations carried out at the request of law enforcement agencies in Polish scientific institutions. The article indicates that the results of examination of gunshot wounds suffered by people in various circumstances may be used for the purpose of issuing forensic veterinary opinions, just as the results of examination of gunshot wounds of large mammals may be helpful in examining the effects of gunshot injuries in humans.

scholarly journals Towards a complex systems approach in sports injury research: simulating running-related injury development with agent-based modelling

2018 ◽  
Vol 53 (9) ◽  
pp. 560-569 ◽  
Author(s):  
Adam Hulme ◽  
Jason Thompson ◽  
Rasmus Oestergaard Nielsen ◽  
Gemma J M Read ◽  
Paul M Salmon
Keyword(s):  
Complex Systems ◽  
Systems Approach ◽  
Computational Modelling ◽  
Sports Injury ◽  
Physical Workload ◽  
Complex Nature ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Starting Point ◽  
Injury Research

ObjectivesThere have been recent calls for the application of the complex systems approach in sports injury research. However, beyond theoretical description and static models of complexity, little progress has been made towards formalising this approach in way that is practical to sports injury scientists and clinicians. Therefore, our objective was to use a computational modelling method and develop a dynamic simulation in sports injury research.MethodsAgent-based modelling (ABM) was used to model the occurrence of sports injury in a synthetic athlete population. The ABM was developed based on sports injury causal frameworks and was applied in the context of distance running-related injury (RRI). Using the acute:chronic workload ratio (ACWR), we simulated the dynamic relationship between changes in weekly running distance and RRI through the manipulation of various ‘athlete management tools’.ResultsThe findings confirmed that building weekly running distances over time, even within the reported ACWR ‘sweet spot’, will eventually result in RRI as athletes reach and surpass their individual physical workload limits. Introducing training-related error into the simulation and the modelling of a ‘hard ceiling’ dynamic resulted in a higher RRI incidence proportion across the population at higher absolute workloads.ConclusionsThe presented simulation offers a practical starting point to further apply more sophisticated computational models that can account for the complex nature of sports injury aetiology. Alongside traditional forms of scientific inquiry, the use of ABM and other simulation-based techniques could be considered as a complementary and alternative methodological approach in sports injury research.

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