109 research outputs found
Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.
UnlabelledDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.ImportanceThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
The standard approach to analyzing 16S tag sequence data, which relies on
clustering reads by sequence similarity into Operational Taxonomic Units
(OTUs), underexploits the accuracy of modern sequencing technology. We present
a clustering-free approach to multi-sample Illumina datasets that can identify
independent bacterial subpopulations regardless of the similarity of their 16S
tag sequences. Using published data from a longitudinal time-series study of
human tongue microbiota, we are able to resolve within standard 97% similarity
OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S
tags differing by as little as 1 nucleotide (99.2% similarity). A comparative
analysis of oral communities of two cohabiting individuals reveals that most
such subpopulations are shared between the two communities at 100% sequence
identity, and that dynamical similarity between subpopulations in one host is
strongly predictive of dynamical similarity between the same subpopulations in
the other host. Our method can also be applied to samples collected in
cross-sectional studies and can be used with the 454 sequencing platform. We
discuss how the sub-OTU resolution of our approach can provide new insight into
factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures +
supplement. Significantly revised for clarity, references added, results not
change
Technology-Rich Ethnography for Examining the Transition to Authentic Problem-Solving in a High School Computer Programming Class
This study utilized elements of technology-rich ethnography to create a rich description of a multi-user virtual environment in a high school computer programming class. Of particular interest was the transition that took place in classroom culture from one characterized by a well-defined problem solving approach to one more indicative of open learning environment. Using technology, high school students created learning activities and resources for use by younger students in the virtual environment. Evidence supported that high school students initially benefitted from the new open environment; however, some immutable elements of the classroom environment presented barriers to peer collaboration and motivation for high-level, creative work. Our findings lend support to the argument that teachers in high school computer programming classes should incorporate the following features in their curricula: open-ended problem solving, real-world clients, group work, student autonomy and ample opportunities for student creative expression.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline
A modest start, but a steady rise in research use: a longitudinal study of nurses during the first five years in professional life
<p>Abstract</p> <p>Background</p> <p>Newly graduated nurses are faced with a challenging work environment that may impede their ability to provide evidence-based practice. However, little is known about the trajectory of registered nurses' use of research during the first years of professional life. Thus, the aim of the current study was to prospectively examine the extent of nurses' use of research during the first five years after undergraduate education and specifically assess changes over time.</p> <p>Method</p> <p>Survey data from a prospective cohort of 1,501 Swedish newly graduated nurses within the national LANE study (Longitudinal Analyses of Nursing Education and Entry in Worklife) were used to investigate perceived use of research over the first five years as a nurse. The dependent variables consisted of three single items assessing instrumental, conceptual, and persuasive research use, where the nurses rated their use on a five-point scale, from 'never' (1) to 'on almost every shift' (5). These data were collected annually and analyzed both descriptively and by longitudinal growth curve analysis.</p> <p>Results</p> <p>Instrumental use of research was most frequently reported, closely followed by conceptual use, with persuasive use occurring to a considerably lower extent. The development over time showed a substantial general upward trend, which was most apparent for conceptual use, increasing from a mean of 2.6 at year one to 3.6 at year five (unstandardized slope +0.25). However, the descriptive findings indicated that the increase started only after the second year. Instrumental use had a year one mean of 2.8 and a year five mean of 3.5 (unstandardized slope +0.19), and persuasive use showed a year one mean of 1.7 and a year five mean of 2.0 (unstandardized slope +0.09).</p> <p>Conclusion</p> <p>There was a clear trend of increasing research use by nurses during their first five years of practice. The level of the initial ratings also indicated the level of research use in subsequent years. However, it took more than two years of professional development before this increase 'kicked in.' These findings support previous research claiming that newly graduated nurses go through a 'transition shock,' reducing their ability to use research findings in clinical work.</p
Patient reported outcome measures for measuring dignity in palliative and end of life care: a scoping review
Experience of parents who have suffered a perinatal death in two Spanish hospitals: a qualitative study
Background: Perinatal grief is a process that affects families in biological, psychological, social and spiritual terms. It is estimated that every year there are 2.7 million perinatal deaths worldwide and 4.43 deaths for every 1000 births in Spain. The aim of this study is to describe and understand the experiences and perceptions of parents who have suffered a perinatal death. Methods: A qualitative study based on Gadamerâs hermeneutic phenomenology. The study was conducted in two hospitals in the South of Spain. Thirteen mothers and eight fathers who had suffered a perinatal death in the 5 years prior to the study participated in this study. In-depth interviews were carried out for data collection. Inductive analysis was used to find themes based on the data. Results: Eight sub-themes emerged, and they were grouped into three main themes: âPerceiving the threat and anticipating the babyâs death: âSomething is going wrong in my pregnancyââ; âEmotional outpouring: the shock of losing a baby and the pain of giving birth to a stillborn babyâ; âWe have had a babyâ: The need to give an identity to the baby and legitimise griefâ. Conclusion: The grief suffered after a perinatal death begins with the anticipation of the death, which relates to the motherâs medical history, symptoms and premonitions. The confirmation of the death leads to emotional shock, characterised by pain and suffering. The chance to take part in mourning rituals and give the baby the identity of a deceased baby may help in the grieving and bereavement process. Having empathy for the parents and notifying them of the death straightaway can help ease the pain. Midwives can help in the grieving process by facilitating the farewell rituals, accompanying the family, helping in honouring the memory of the baby, and supporting parents in giving the deceased infant an identity that makes them a family member
From Geocentrism to Allocentrism: Teaching the Phases of the Moon in a Digital Full-Dome Planetarium
Time series data for Canadian arctic vertebrates: IPY contributions to science, management, and policy
Data Descriptor: A global multiproxy database for temperature reconstructions of the Common Era
Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high-and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.(TABLE)Since the pioneering work of D'Arrigo and Jacoby1-3, as well as Mann et al. 4,5, temperature reconstructions of the Common Era have become a key component of climate assessments6-9. Such reconstructions depend strongly on the composition of the underlying network of climate proxies10, and it is therefore critical for the climate community to have access to a community-vetted, quality-controlled database of temperature-sensitive records stored in a self-describing format. The Past Global Changes (PAGES) 2k consortium, a self-organized, international group of experts, recently assembled such a database, and used it to reconstruct surface temperature over continental-scale regions11 (hereafter, ` PAGES2k-2013').This data descriptor presents version 2.0.0 of the PAGES2k proxy temperature database (Data Citation 1). It augments the PAGES2k-2013 collection of terrestrial records with marine records assembled by the Ocean2k working group at centennial12 and annual13 time scales. In addition to these previously published data compilations, this version includes substantially more records, extensive new metadata, and validation. Furthermore, the selection criteria for records included in this version are applied more uniformly and transparently across regions, resulting in a more cohesive data product.This data descriptor describes the contents of the database, the criteria for inclusion, and quantifies the relation of each record with instrumental temperature. In addition, the paleotemperature time series are summarized as composites to highlight the most salient decadal-to centennial-scale behaviour of the dataset and check mutual consistency between paleoclimate archives. We provide extensive Matlab code to probe the database-processing, filtering and aggregating it in various ways to investigate temperature variability over the Common Era. The unique approach to data stewardship and code-sharing employed here is designed to enable an unprecedented scale of investigation of the temperature history of the Common Era, by the scientific community and citizen-scientists alike
Educational Uses of Virtual Reality Technology
Educating current and future generations of American children to live in an information society is a critical issue. It is compounded by the recognized need to provide life-long education for all citizens and to support a flexible workforce. Virtual reality (VR) technology has been widely proposed as a major technological advance that can offer significant support for such education. There are several ways in which VR technology is expected to facilitate learning. One of its unique capabilities is the ability to allow students to visualize abstract concepts, to observe events at atomic or planetary scales, and to visit environments and interact with events that distance, time, or safety factors make unavailable. The types of activities supported by this capability facilitate current educational thinking that students are better able to master, retain, and generalize new knowledge when they are actively involved in constructing that knowledge in a learning-by-doing situation. The potential of VR technology for supporting education is widely recognized. Several programs designed to introduce large numbers of students and teachers to the technology have been established, a number of academic institutions have developed research programs to investigate key issues, and some public schools are evaluating the technology
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