scholarly journals Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes

2016 ◽  
Author(s):  
Gregorio Iraola ◽  
Hugo Naya
Keyword(s):  
Best Practices ◽  
Polyphasic Taxonomy ◽  
Bacterial Species ◽  
Genomic Data ◽  
Link Type ◽  
Prokaryotic Genomes ◽  
Functional Features ◽  
Definition Of ◽  
Ecological Coherence ◽  
Metabolic Signatures

Taxonomy of prokaryotes has remained a controversial discipline due to the extreme plasticity of microorganisms, causing inconsistencies between phenotypic and genotypic classifications. The genomics era has enhanced taxonomy but also opened new debates about the best practices for incorporating genomic data into polyphasic taxonomy protocols, which are fairly biased towards the identification of bacterial species. Here we use an extensive dataset of Archaea and Bacteria to prove that metabolic signatures coded in their genomes are informative traits that allow to accurately classify organisms coherently to higher taxonomic ranks, and to associate functional features with the definition of taxa. Our results support the ecological coherence of higher taxonomic ranks and reconciles taxonomy with traditional chemotaxonomic traits inferred from genomes. KARL, a simple and free tool useful for assisting polyphasic taxonomy or to perform functional prospections is also presented (https://github.com/giraola/KARL).

scholarly journals rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree

2018 ◽  
Author(s):  
Alexander M. Wailan ◽  
Francesc Coll ◽  
Eva Heinz ◽  
Gerry Tonkin-Hill ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Phylogenetic Tree ◽  
Bacterial Species ◽  
Genomic Data ◽  
Transmission Dynamics ◽  
Whole Genome Sequence ◽  
List Type ◽  
Bacterial Populations ◽  
Link Type ◽  
Hospital Outbreak

ABSTRACTThe ability to distinguish between pathogens is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances, remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this program was demonstrated using genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically-confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.DATA SUMMARYSource code for rPinecone is available on GitHub under the open source licence GNU GPL 3; (url: https://github.com/alexwailan/rpinecone).Newick format files for both phylogenetic trees have been deposited in Figshare; (url: https://doi.org/10.6084/m9.figshare.7022558)Geographical analysis of the S. Typhi Dataset using Microreact is available at https://microreact.org/project/r1IqkrN1X.Accession numbers, meta data and sample lineage results of both datasets used in this paper are listed in the supplementary tables.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTWhole genome sequence data from bacterial pathogens is increasingly used in the epidemiological investigation of infectious disease, both in outbreak and endemic situations. However, distinguishing bacterial species which are both very similar and which are likely to come from a small geographical and temporal range presents a major technical challenge for epidemiologists. rPinecone was designed to address this challenge and utilises phylogenetic data to define lineages within bacterial populations that have limited variation. This approach is therefore of great interest to epidemiologists as it adds a further level of clarity above and beyond that which is offered by existing approaches which have not been designed to consider bacterial isolates containing variation that only transiently exist, but which is epidemiologically informative. rPinecone has the flexibility to be applied to multiple pathogens and has direct application for investigations of clinical outbreaks and endemic disease to understand transmission dynamics or geographical hotspots of disease.

A Unifying Principle for a Researcher Learning Safety: Reduce Uncertainty!

2018 ◽  
Author(s):  
Camilla Kao ◽  
Russell Furr
Keyword(s):  
Decision Making ◽  
Best Practices ◽  
Mission Statement ◽  
Safety Information ◽  
Health And Safety ◽  
Mission Statements ◽  
Definition Of ◽  
Physical And Chemical

Conveying safety information to researchers is challenging. A list of rules and best practices often is not remembered thoroughly even by individuals who want to remember everything. Researchers in science thinking according to principles: mathematical, physical, and chemical laws; biological paradigms. They use frameworks and logic, rather than memorization, to achieve the bulk of their work. Can safety be taught to researchers in a manner that matches with how they are trained to think? Is there a principle more defined than "Think safety!" that can help researchers make good decisions in situations that are complex, new, and demanding?<div><br></div><div>Effective trainings in other professions can arise from the use of a mission statement that participants internalize as a mental framework or model for future decision-making. We propose that mission statements incorporating the concept of <b>reducing uncertainty</b> could provide such a framework for learning safety. This essay briefly explains the definition of <b>uncertainty</b> in the context of health and safety, discusses the need for an individual to <b>personalize</b> a mission statement in order to internalize it, and connects the idea of <b>greater control</b> over a situation with less uncertainty with respect to safety. The principle of reducing uncertainty might also help <b>non-researchers</b> think about safety. People from all walks of life should be able to understand that more control over their situations provides more protection for them, their colleagues, and the environment.</div>

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

scholarly journals Are Best Practices Really Best? A Review of the Best Practices Literature in Library and Information Studies

2013 ◽  
Vol 8 (4) ◽  
pp. 110 ◽  
Author(s):  
Jackie Druery ◽  
Nancy McCormack ◽  
Sharon Murphy
Keyword(s):  
Best Practices ◽  
Best Practice ◽  
Information Science ◽  
Library And Information Science ◽  
Science Literature ◽  
Common Definition ◽  
Library And Information Studies ◽  
Information Studies ◽  
The Subject ◽  
Definition Of

Objective - The term “best practice” appears often in library and information science literature, yet, despite the frequency with which the term is used, there is little discussion about what is meant by the term and how one can reliably identify a best practice. Methods – This paper reviews 113 articles that identify and discuss best practices, in order to determine how “best practices” are distinguished from other practices, and whether these determinations are made on the basis of consistent and reliable evidence. The review also takes into account definitions of the term to discover if a common definition is used amongst authors. Results – The “evidence” upon which papers on “best practices” are based falls into one of the following six categories: 1) opinion (n=18, 15%), 2) literature reviews (n=13, 12%), 3) practices in the library in which the author works (n=19, 17%), 4) formal and informal qualitative and quantitative approaches (n=16, 14%), 5) a combination of the aforementioned (i.e., combined approaches) (n=34, 30%), and 6) “other” sources or approaches which are largely one of a kind (n=13, 12%). There is no widely shared or common definition of “best practices” amongst the authors of these papers, and most papers (n=94, 83%) fail to define the term at all. The number of papers was, for the most part, split evenly amongst the six categories indicating that writers on the subject are basing “best practices” assertions on a wide variety of sources and evidence. Conclusions – Library and information science literature on “best practices” is rarely based on rigorous empirical methods of research and therefore is generally unreliable. There is, in addition, no widely held understanding of what is meant by the use of the term.

scholarly journals Good practices in collecting umbilical cord and placental blood

2016 ◽  
Vol 24 (0) ◽  
Author(s):  
Lauren Auer Lopes ◽  
Elizabeth Bernardino ◽  
Karla Crozeta ◽  
Paulo Ricardo Bittencourt Guimarães
Keyword(s):  
Best Practices ◽  
Umbilical Cord ◽  
Management Tool ◽  
Blood Collection ◽  
Placental Blood ◽  
Operational Factors ◽  
Blood Specimens ◽  
Definition Of ◽  
Gathering Data

Abstract Objective: to identify the factors related to the quality of umbilical cord and placental blood specimens, and define best practices for their collection in a government bank of umbilical cord and placental blood. Method: this was a descriptive study, quantitative approach, performed at a government umbilical cord and placental blood bank, in two steps: 1) verification of the obstetric, neonatal and operational factors, using a specific tool for gathering data as non-participant observers; 2) definition of best practices by grouping non-conformities observed before, during and after blood collection. The data was analyzed using descriptive statistics and the following statistical software: Statistica(r) and R(r). Results: while there was a correlation with obstetrical and neonatal factors, there was a larger correlation with operational factors, resulting in the need to adjust the professional practices of the nursing staff and obstetrical team involved in collecting this type of blood. Based on these non-conformities we defined best practices for nurses before, during and after blood collection. Conclusion: the best practices defined in this study are an important management tool for the work of nurses in obtaining blood specimens of high cell quality.

scholarly journals Strengthening the SSTC NRS Scientific and Technical Potential through Participation in the IAEA Coordinated Research Projects

2021 ◽  
pp. 5-13
Author(s):  
Yu. Balashevska ◽  
D. Gumenyuk ◽  
Iu. Ovdiienko ◽  
O. Pecherytsia ◽  
I. Shevchenko ◽  
...  
Keyword(s):  
Best Practices ◽  
Safety Assessment ◽  
Radiation Safety ◽  
Research Projects ◽  
Spent Fuel ◽  
Research Activities ◽  
Technical Potential ◽  
Technical Issues ◽  
Fuel Characterization ◽  
Definition Of

The State Scientific and Technical Center for Nuclear and Radiation Safety (SSTC NRS), a Ukrainian enterprise with a 29-year experience in the area of scientific and technical support to the national nuclear regulator (SNRIU), has been actively involved in international research activities. Participation in the IAEA coordinated research activities is among the SSTC NRS priorities. In the period of 2018–2020, the IAEA accepted four SSTC NRS proposals for participation in respective Coordinated Research Projects (CRPs). These CRPs address scientific and technical issues in different areas such as: 1) performance of probabilistic safety assessment for multi-unit/multi-reactor sites; 2) use of dose projection tools to ensure preparedness and response to nuclear and radiological emergencies; 3) phenomena related to in-vessel melt retention; 4) spent fuel characterization. This article presents a brief overview of the abovementioned projects with definition of scientific contributions by the SSTC NRS (participation in benchmarks, development of methodological documents on implementing research stages and of IAEA technical documents (TECDOC) for demonstration of best practices and results of research carried out by international teams).

scholarly journals chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

2017 ◽  
Author(s):  
Mickael Silva ◽  
Miguel Machado ◽  
Diogo N. Silva ◽  
Mirko Rossi ◽  
Jacob Moran-Gilad ◽  
...  
Keyword(s):  
Open Source ◽  
Core Genome ◽  
Bacterial Species ◽  
Outbreak Detection ◽  
Strain Identification ◽  
List Type ◽  
Whole Genome ◽  
Link Type ◽  
The Creation ◽  
Allele Calling

ABSTRACTGene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available athttps://github.com/B-UMMI/chewBBACAor as a docker image athttps://hub.docker.com/r/ummidock/chewbbaca/.DATA SUMMARYAssembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted asStreptococcus agalactiaetaxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.Code for the chewBBACA suite is available athttps://github.com/B-UMMI/chewBBACAwhile the tutorial example is found athttps://github.com/B-UMMI/chewBBACA_tutorial.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTThe chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.

scholarly journals Neuroeducation: Integrating Brain-Based Psychoeducation into Clinical Practice

2016 ◽  
Vol 38 (2) ◽  
pp. 103-115 ◽  
Author(s):  
Raissa Miller
Keyword(s):  
Mental Health ◽  
Clinical Practice ◽  
Best Practices ◽  
Clinical Assessment ◽  
Mental Health Counselors ◽  
Counselor Competence ◽  
Effective Interventions ◽  
Neuroscience Research ◽  
Definition Of ◽  
Learning Principles

Understanding and integrating neuroscience research into clinical practice represents a rapidly growing area in mental health. An expanding body of neuroscience literature increasingly informs clinical practice by validating theory, guiding clinical assessment and conceptualization, directing effective interventions, and facilitating cross-disciplinary communication. Little attention, however, has been given to the use of neuroeducation with clients. In this article, the author provides mental health counselors with a definition of neuroeducation and a rationale for incorporating neuroeducation into clinical practice. The author identifies common neuroeducation topics and offers activity suggestions to illustrate their use in counseling. Finally, the author offers best practices for implementing neuroeducation, including attention to counselor competence, client readiness, and neuroscience of learning principles. Implications for research are also discussed.

scholarly journals From symptomatic to pre-symptomatic patient: the tide of personal genomics

2011 ◽  
Vol 10 (03) ◽  
pp. C03
Author(s):  
Marina Levina ◽  
Roswell Quinn
Keyword(s):  
Human Subjects ◽  
Genomic Data ◽  
Symptomatic Patient ◽  
Privacy Rights ◽  
Personal Genomics ◽  
Direct To Consumer ◽  
Marketing Social ◽  
Genomics Research ◽  
Definition Of ◽  
Consumer Marketing

Personal Genomics Companies are an emerging form of biotechnology startup that bring rapidly advancing whole genome technologies to a variety of commercial venues. With a combination of direct-to-consumer marketing, social media, and Web 2.0 applications these companies seek to create novel uses, including entertainment, for what is described as predictive medicine – that is the use of genetic marketers to create health forecasts that would allow individual’s healthcare to be tailored to their individual genomic data. In this brief piece, the authors use a critical cultural approach to question how this combination of genomics research, marketing, and communications technologies may alter both patient experiences and research processes. In it we argue these companies radically expand the definition of a patient by claiming all consumers are simply pre-symptomatic patients. Moreover, by placing genomic data on both the marketplace and cyberspace, personal genomic companies seek to create new avenues of research that alter how we define (and access) research agendas and human subjects. Therefore, beyond commonly discussed issues of ethics and privacy rights, Personal Genomics has the potential to alter both healthcare priorities and distribution.

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