scholarly journals Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Delphine Larivière ◽  
Laura Wickham ◽  
Kenneth Keiler ◽  
Anton Nekrutenko ◽  
Keyword(s):  
Data Analysis ◽  
Promoter Sequence ◽  
Entire Genome ◽  
Link Type ◽  
Transposon Insertion ◽  
Control Procedures ◽  
Reproducible Analysis ◽  
Using Data ◽  
Transposon Insertion Sequencing ◽  
The Impact

Abstract Background Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools, is hindered by local computational resource limitations, and does not offer widely accepted standards. One such “problem areas” is the analysis of Transposon Insertion Sequencing (TIS) data. TIS allows probing of almost the entire genome of a microorganism by introducing random insertions of transposon-derived constructs. The impact of the insertions on the survival and growth under specific conditions provides precise information about genes affecting specific phenotypic characteristics. A wide array of tools has been developed to analyze TIS data. Among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. Results Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies, we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures, such as determining the optimal tool parameters for the analysis and removal of contamination. Conclusions Our work provides an assessment of the currently available tools for TIS data analysis. It offers ready to use workflows that can be invoked by anyone in the world using our public Galaxy platform (https://usegalaxy.org). To lower the entry barriers, we have also developed interactive tutorials explaining details of TIS data analysis procedures at https://bit.ly/gxy-tis.

scholarly journals Reproducible and accessible analysis of transposon insertion data at scale

2020 ◽  
Author(s):  
Delphine Larivière ◽  
Laura Wickham ◽  
Kenneth C. Keiler ◽  
Anton Nekrutenko
Keyword(s):  
Quality Control ◽  
Data Analysis ◽  
Promoter Sequence ◽  
Read Count ◽  
Transposon Insertion ◽  
Sequence Identification ◽  
Control Procedures ◽  
Reproducible Analysis ◽  
Using Data

ABSTRACTSignificant progress has been made in advancing and standardizing tools for human genomic and biomedical research, yet the field of next generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools, is hindered by local computational resource limitations, and does not offer widely accepted standards. One of such “problem areas” is the analysis of Transposon Insertion Sequencing (TIS) data. TIS allows perturbing the entire genome of a microorganism by introducing random insertions of transposon-derived constructs. The impact of the insertions on the survival and growth provides precise information about genes affecting specific phenotypic characteristics. A wide array of tools has been developed to analyze TIS data and among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures such as the determination of the optimal tool parameters for the analysis and removal of contamination. Our work provides an assessment of the currently available tools for TIS data analysis and offers ready to use workflows that can be invoked by anyone in the world using our public Galaxy platform (https://usegalaxy.org). To lower the entry barriers we have also developed interactive tutorials explaining details of TIS data analysis procedures at https://bit.ly/gxy-tis.ImportanceA wide array of tools has been developed to analyze TIS data and among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures such as the determination of the optimal tool parameters for the analysis and removal of contamination. Our work democratizes the TIS data analysis by providing open workflows supported by public computational infrastructure.

scholarly journals In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes

2021 ◽  
Author(s):  
Lucas Morinière ◽  
Solène Lecomte ◽  
Erwan Gueguen ◽  
Franck Bertolla
Keyword(s):  
Comparative Genomics ◽  
Plant Pathogen ◽  
Type Species ◽  
Essential Genes ◽  
Content Type ◽  
Link Type ◽  
Transposon Insertion ◽  
Ecological Features ◽  
Genomic Study ◽  
Transposon Insertion Sequencing

The essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome ofXanthomonas hortorumpv.vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativaL.) which belongs to the plant-pathogen reservoir genusXanthomonasand is affiliated to the familyXanthomonadaceae. No practical means of disease control or prevention against this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome ofX. hortorumpv.vitiansLM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features ofXanthomonasorXanthomonadaceaespecies, or acquired through horizontal gene transfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study ofX. hortorumpv.vitians.

scholarly journals The impact of the oil palm plantation area on the community economy in East Kutai Regency, East

2020 ◽  
Vol 9 (4) ◽  
pp. 130-137
Author(s):  
Zulkarnain Zulkarnain
Keyword(s):  
Data Analysis ◽  
Sampling Method ◽  
Community Economy ◽  
Plantation Development ◽  
Regional Influence ◽  
The Difference ◽  
Using Data ◽  
The Cost ◽  
The Impact ◽  
Data Analysis Methods

This article is about how the impact of change and the extent of existing activities contribute to the surrounding community. The development of large private plantations in the East Kutai Regency has also been inseparable from problems, especially in the management of plasma plantations carried out by large plantation companies. Issues that arise include the difference in productivity between nucleus and plasma plantations, the low acceptance of plasma farmers so that it is considered not to improve the welfare of the community. The purpose of this study was to determine the impact of large private plantations on community welfare, evaluating the implementation of plantation development activities in the East Kutai Regency. The sampling method is done by purposed sampling using data analysis methods, the analysis of the cost of the benefits of the area, the analysis of the level of welfare, and analysis of regional influence. With the results of the study as follows: the cost of benefits is positive; the multiplier value is 2,614 and the value of NTM is 0.37.

DAMPAK GEMPA BUMI LOMBOK TERHADAP KONDISI SOSIAL EKONOMI MASYARAKAT DI DESA KEKAIT KECAMATAN GUNUNG SARI KABUPATEN LOMBOK BARAT

2019 ◽  
Vol 1 (2) ◽  
pp. 210-227
Author(s):  
Laluiwan Eko Jakandar
Keyword(s):  
Data Analysis ◽  
Secondary Data ◽  
Research Area ◽  
Economic Life ◽  
Economic Downturn ◽  
Social Activities ◽  
Reconstruction Process ◽  
Mutual Cooperation ◽  
Using Data ◽  
The Impact

This study aims to determine the impact or effect of the Lombok 2018 earthquake on the socio-economic life of the community in Kekait Village, Gunung Sari District, West Lombok Regency and find out the efforts made by the community in Kekait Village, Gunung Sari District, West Lombok Regency to rise from adversity due to the Lombok earthquake 2018 that happened. This study included research using a qualitative descriptive approach with a double embedded case study strategy. Data is taken from primary and secondary data. While the data sources in this study are informants or informants, events and activities as well as documents and archives. Test data validity is done by using data or source triangulation techniques and method triangulation. Data analysis uses interactive data analysis techniques with stages, namely: data collection, data reduction, data presentation, drawing conclusions and verification. The results of the study show that the impact of the earthquake on the Kekait Village community has had a tremendous impact on their lives. The August 5 2018 earthquake has a serious impact, especially the economic paralysis which results in every citizen living in an "invalid capital" situation or living without income at all, which applies to at least three community groups including entrepreneurship, farmers, and laborers. While other impacts of social activities such as social gathering, mutual cooperation, tahlilan and ruwahan in the research area had been halted after the earthquake because there was no room to carry out these activities. Social activities will begin to be implemented again after the reconstruction process is complete. There are three strategies that are carried out by the kepuh community. The link in the effort to rise from the economic downturn includes: First, psychological efforts. Second, religious efforts. Third economic effort

scholarly journals Optimization Modeling and Empirical Research on Gasoline Octane Loss Based on Data Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Ji Guo ◽  
Yujia Lou ◽  
Wanyi Wang ◽  
Xianhua Wu
Keyword(s):  
Data Analysis ◽  
Catalytic Cracking ◽  
Economic Cost ◽  
Petroleum Products ◽  
Operating Conditions ◽  
Atmospheric Environment ◽  
Optimal Operating ◽  
Operating Variables ◽  
Using Data ◽  
The Impact

Gasoline is one of the most consumed light petroleum products in transportation and other industries. This paper proposes a method for optimizing gasoline octane loss using data analysis technology aimed at optimizing the production process and minimizing the loss of gasoline octane. Firstly, the data are screened and the high-dimensional data are reduced to construct the neural network prediction model optimized by genetic algorithm. After utilizing the model for prediction, the optimal operating condition is achieved. Secondly, ensuring that the gasoline emission meets the standard, the octane loss is reduced by adjusting the operating variables. Thirdly, actual data are collected and calculated to obtain the main operating variables and their optimal operating conditions of a petrochemical company affecting the catalytic cracking gasoline S-Zorb unit, thus providing companies using S-Zorb units with reference data for optimizing gasoline catalytic cracking processes. Fourthly, the superiority of the proposed method was verified by comparing it with the other methods. This paper intends to contribute to better modeling the progress of gasoline catalytic cracking by adequately considering the impact of multiple factors, improving the quality of refined oil products of chemical enterprises, saving the economic cost of chemical enterprises, and protecting the atmospheric environment.

Accent Policy and Accent Modification Enterprises as Potential Indicators of Intercultural Power Relations: A Call for an Updated Research Agenda

2013 ◽  
Vol 3 (1) ◽  
pp. 22-33 ◽  
Author(s):  
Brynne D. Ovalle ◽  
Rahul Chakraborty
Keyword(s):  
International Relations ◽  
Identity Construction ◽  
Social Theory ◽  
Power Relations ◽  
Linguistic Diversity ◽  
Cultural Organization ◽  
Using Data ◽  
The Individual ◽  
The Impact ◽  
The Relationship

This article has two purposes: (a) to examine the relationship between intercultural power relations and the widespread practice of accent discrimination and (b) to underscore the ramifications of accent discrimination both for the individual and for global society as a whole. First, authors review social theory regarding language and group identity construction, and then go on to integrate more current studies linking accent bias to sociocultural variables. Authors discuss three examples of intercultural accent discrimination in order to illustrate how this link manifests itself in the broader context of international relations (i.e., how accent discrimination is generated in situations of unequal power) and, using a review of current research, assess the consequences of accent discrimination for the individual. Finally, the article highlights the impact that linguistic discrimination is having on linguistic diversity globally, partially using data from the United Nations Educational, Scientific and Cultural Organization (UNESCO) and partially by offering a potential context for interpreting the emergence of practices that seek to reduce or modify speaker accents.

Interculturalism and the Acceptance of Minority Groups

2020 ◽  
Vol 51 (2) ◽  
pp. 135-140 ◽  
Author(s):  
Maykel Verkuyten ◽  
Kumar Yogeeswaran
Keyword(s):  
Minority Groups ◽  
Psychological Research ◽  
Survey Experiment ◽  
Social Psychological ◽  
Negative Attitudes ◽  
Positive Attitudes ◽  
Social Psychological Research ◽  
Using Data ◽  
The Impact ◽  
Situational Effect

Abstract. Multiculturalism has been criticized and rejected by an increasing number of politicians, and social psychological research has shown that it can lead to outgroup stereotyping, essentialist thinking, and negative attitudes. Interculturalism has been proposed as an alternative diversity ideology, but there is almost no systematic empirical evidence about the impact of interculturalism on the acceptance of migrants and minority groups. Using data from a survey experiment conducted in the Netherlands, we examined the situational effect of promoting interculturalism on acceptance. The results show that for liberals, but not for conservatives, interculturalism leads to more positive attitudes toward immigrant-origin groups and increased willingness to engage in contact, relative to multiculturalism.

INDONESIA LANGUAGE INTERFERENCE FORM IN BASIC PPL LEARNING THAILAND UNHASY COLLEGE SYUDENTS

2020 ◽  
Vol 8 (2) ◽  
pp. 38
Author(s):  
Siti Mariana Ulfa
Keyword(s):  
Qualitative Research ◽  
Data Analysis ◽  
Data Collection ◽  
Teaching Practice ◽  
Data Presentation ◽  
Analysis Techniques ◽  
Thai Students ◽  
The Impact ◽  
Collection Methods ◽  
Recording Techniques

AbstractHumans on earth need social interaction with others. Humans can use more than one language in communication. Thus, the impact that arises when the use of one or more languages is the contact between languages. One obvious form of contact between languages is interference. Interference can occur at all levels of life. As in this study, namely Indonesian Language Interference in Learning PPL Basic Thailand Unhasy Students. This study contains the form of interference that occurs in Thai students who are conducting teaching practices in the classroom. This type of research is descriptive qualitative research that seeks to describe any interference that occurs in the speech of Thai students when teaching practice. Data collection methods in this study are (1) observation techniques, (2) audio-visual recording techniques using CCTV and (3) recording techniques, by recording all data that has been obtained. Whereas the data wetness uses, (1) data triangulation, (2) improvement in perseverance and (3) peer review through discussion. Data analysis techniques in this study are (1) data collection, (2) data reduction, (3) data presentation and (4) conclusions. It can be seen that the interference that occurs includes (1) interference in phonological systems, (2) interference in morphological systems and (3) interference in syntactic systems. 

AKTUALISASI PEDIDIKAN KARAKTER DALAM PENGEMBANGAN REVOLUSI MENTAL BERBASIS ADIWIYATA DAN MULTIKULTURAL

2018 ◽  
Vol 2 (2) ◽  
Author(s):  
Suhardi Suhardi
Keyword(s):  
Data Analysis ◽  
Character Education ◽  
Achievement Motivation ◽  
Case Study Research ◽  
Individual Development ◽  
Human Beings ◽  
Soft Skill ◽  
Design Data ◽  
Strategic Role ◽  
Using Data

Mental revolution of education requires efforts to print educated human beings by having the motivation to meet the standards of achievement excellence, such as ethos of progress, ethics, achievement motivation, discipline, optimistic, productive, innovative and active views. This can be implemented with character education. Character education is one of the soft skill tools that can be integrated in learning in each subject. Learning activities using an active learning approach have a strategic role in instilling national character values so that students are able to behave and act on values that have become their personality. The purpose of this study was to find and analyze about: 1) Implementation of Character Education to Build Adiwiyata-Based Mental Revolution and Multiculturalism; 2) Implementation of Character Education to Build Mental Revolution in Organizational Culture. This study uses a qualitative approach with phenomenological naturatistics (phenomenology approach), with a descriptive type of case study research design. Data were analyzed using data analysis techniques: data reduction, data analysis and conclusions. The results of the study are: The application of character education to develop a mental revolution can be started from the character of building the environment. Environmental character is very important for individual development. The implementation of character education in building a mental revolution can emphasize the internalization of multicultural values and Adiwiyata which in the end will form a loving environmental awareness and foster a spirit of tolerance.

International Remittances and Private Healthcare in Kerala, India

2020 ◽  
Vol 17 (3) ◽  
pp. 445-460
Author(s):  
Mohd Imran Khan ◽  
Valatheeswaran C.
Keyword(s):  
Instrumental Variable ◽  
Capital Investment ◽  
Healthcare Expenditure ◽  
Healthcare Services ◽  
Private Healthcare ◽  
International Remittances ◽  
Variable Approach ◽  
Using Data ◽  
The Impact ◽  
Instrumental Variable Approach

The inflow of international remittances to Kerala has been increasing over the last three decades. It has increased the income of recipient households and enabled them to spend more on human capital investment. Using data from the Kerala Migration Survey-2010, this study analyses the impact of remittance receipts on the households’ healthcare expenditure and access to private healthcare in Kerala. This study employs an instrumental variable approach to account for the endogeneity of remittances receipts. The empirical results show that remittance income has a positive and significant impact on households’ healthcare expenditure and access to private healthcare services. After disaggregating the sample into different heterogeneous groups, this study found that remittances have a greater effect on lower-income households and Other Backward Class (OBC) households but not Scheduled Caste (SC) and Scheduled Tribe (ST) households, which remain excluded from reaping the benefit of international migration and remittances.

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