Short-insert libraries as a method of problem solving in genome sequencing.
Ontology highlight
ABSTRACT:
SUBMITTER: McMurray AA
PROVIDER: S-EPMC310723 | biostudies-literature | 1998 May
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Massively parallel, second-generation short-read DNA sequencing has become an integral tool in biology for genomic studies. Offering highly accurate base-pair resolution at the most competitive price, the technology has become widespread. However, high-throughput generation of multiplexed DNA libraries can be costly and cumbersome. Here, we present a cost-conscious protocol for generating multiplexed short-read DNA libraries using a bead-linked transposome from Illumina. We prepare libraries in high-throughput with small reaction volumes that use 1/50th the amount of transposome compared to Illumina DNA Prep tagmentation protocols. By reducing transposome usage and optimising the protocol to circumvent magnetic bead-based clean-ups between steps, we reduce costs, labour time and DNA input requirements. Developing our own dual index primers further reduced costs and enables up to nine 96-well microplate combinations. This facilitates efficient usage of large-scale sequencing platforms, such as the Illumina NovaSeq 6000, which offers up to three terabases of sequencing per S4 flow cell. The protocol presented substantially reduces the cost per library by approximately 1/20th compared to conventional Illumina methods.
| S-EPMC9882895 | biostudies-literature
Project description:Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird
| PRJEB40949 | ENA
Project description:The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.
| S-EPMC3236044 | biostudies-literature
Project description:In this paper we argue that a synthesis of findings across the various sub-areas of research in complex problem solving and consequently progress in theory building is hampered by an insufficient differentiation of complexity and difficulty. In the proposed framework of person, task, and situation (PTS), complexity is conceptualized as a quality that is determined by the cognitive demands that the characteristics of the task and the situation impose. Difficulty represents the quantifiable level of a person's success in dealing with such demands. We use the well-documented "semantic effect" as an exemplar for testing some of the conceptual assumptions derived from the PTS framework. We demonstrate how a differentiation between complexity and difficulty can help take beyond a potentially too narrowly defined psychometric perspective and subsequently gain a better understanding of the cognitive mechanisms behind this effect. In an empirical study a total of 240 university students were randomly allocated to one of four conditions. The four conditions resulted from contrasting the semanticity level of the variable labels used in the CPS system (high vs. low) and two instruction conditions for how to explore the CPS system's causal structure (starting with the assumption that all relationships between variables existed vs. starting with the assumption that none of the relationships existed). The variation in the instruction aimed at inducing knowledge acquisition processes of either (1) systematic elimination of presumptions, or (2) systematic compilation of a mental representation of the causal structure underpinning the system. Results indicate that (a) it is more complex to adopt a "blank slate" perspective under high semanticity as it requires processes of inhibiting prior assumptions, and (b) it seems more difficult to employ a systematic heuristic when testing against presumptions. In combination, situational characteristics, such as the semanticity of variable labels, have the potential to trigger qualitatively different tasks. Failing to differentiate between 'task' and 'situation' as independent sources of complexity and treating complexity and difficulty synonymously threaten the validity of performance scores obtained in CPS research.
| S-EPMC5641385 | biostudies-other
Project description:The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world.
| S-EPMC3475381 | biostudies-literature
Project description:Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
| S-EPMC4128722 | biostudies-literature
Project description:BackgroundParticipation rates in health surveys, recognized as an important quality dimension, have been declining over the years, which may affect representativeness and confidence in results. The Portuguese national health examination survey INSEF (2015) achieved a participation rate of 43.9%, which is in line with participation rates from other similar health examination surveys. The objective of this article is to describe how local teams of survey personnel conducted the survey, describing strategies used to solve practical survey problems and to try to increase the participation rate.MethodsAfter a literature search, informal interviews were conducted with 14 public health officials from local health examination teams, regional and central authorities. Forty-one of the local staff members (survey personnel) also filled in a short questionnaire anonymously. The interviews and self-administered questionnaires were analysed using mixed methods, informed by thematic analysis.ResultsThe local teams believed that the detailed manual, described as a "cookbook for making a health examination survey", made it possible to maintain high scientific standards while allowing for improvising solutions to problems in the local context. The quality of the manual, supported by a series of training workshops with the central research and support team, gave the teams the confidence and knowledge to implement local solutions. Motivation and cohesion within the local teams were among the goals of the training process. Local teams felt empowered by being given large responsibilities and worked hard to incite people to attend the examination through a close and persuasive approach. Local teams praised their INSA contacts for being available for assistance throughout the survey, and said they were inspired to try harder to reach participants to please their contacts for interpersonal reasons.ConclusionsThe theory of organizational improvisation or bricolage, which means using limited resources to solve problems, was useful to discuss and understand what took place during INSEF. A detailed manual covering standard procedures, continuous monitoring of the data collection and face-to-face workshops, including role-play, were vital to assure high scientific standards and high participation rates in this health examination survey. Close contacts between the central team and local focal points in all regions and all survey sites were key to accommodating unexpected challenges and innovative solutions.
| S-EPMC9400230 | biostudies-literature
Project description:According to the restructuring hypothesis, insight problem solving typically progresses through consecutive stages of search, impasse, insight, and search again for someone, who solves the task. The order of these stages was determined through self-reports of problem solvers and has never been verified behaviorally. We asked whether individual analysis of problem solving attempts of participants revealed the same order of problem solving stages as defined by the theory and whether their subjective feelings corresponded to the problem solving stages they were in. Our participants tried to solve the Five-Square problem in an online task, while we recorded the time and trajectory of their stick movements. After the task they were asked about their feelings related to insight and some of them also had the possibility of reporting impasse while working on the task. We found that the majority of participants did not follow the classic four-stage model of insight, but had more complex sequences of problem solving stages, with search and impasse recurring several times. This means that the classic four-stage model is not sufficient to describe variability on the individual level. We revised the classic model and we provide a new model that can generate all sequences found. Solvers reported insight more often than non-solvers and non-solvers reported impasse more often than solvers, as expected; but participants did not report impasse more often during behaviorally defined impasse stages than during other stages. This shows that impasse reports might be unreliable indicators of impasse. Our study highlights the importance of individual analysis of problem solving behavior to verify insight theory.
| S-EPMC4523725 | biostudies-literature
Project description:When confronted with novel problems, problem-solvers must decide whether to copy a modeled solution or to explore their own unique solutions. While past work has established that infants can learn to solve problems both through their own exploration and through imitation, little work has explored the factors that influence which of these approaches infants select to solve a given problem. Moreover, past work has treated imitation and exploration as qualitatively distinct, although these two possibilities may exist along a continuum. Here, we apply a program novel to developmental psychology (DeepLabCut) to archival data (Lucca et al., 2020) to investigate the influence of the effort and success of an adult's modeled solution, and infants' firsthand experience with failure, on infants' imitative versus exploratory problem-solving approaches. Our results reveal that tendencies toward exploration are relatively immune to the information from the adult model, but that exploration generally increased in response to firsthand experience with failure. In addition, we found that increases in maximum force and decreases in trying time were associated with greater exploration, and that exploration subsequently predicted problem-solving success on a new iteration of the task. Thus, our results demonstrate that infants increase exploration in response to failure and that exploration may operate in a larger motivational framework with force, trying time, and expectations of task success.
| S-EPMC8606407 | biostudies-literature
Project description:Behavioural innovations with tool-like objects in non-habitually tool-using species are thought to require complex physical understanding, but the underlying cognitive processes remain poorly understood. A few parrot species are capable of innovating tool-use and borderline tool-use behaviours. We tested this capacity in two species of macaw (Ara ambiguus, n = 9; Ara glaucogularis, n = 8) to investigate if they could solve a problem-solving task through manufacture of a multi-stone construction. Specifically, after having functional experience with a pre-inserted stick tool to push a reward out of a horizontal tube, the subjects were required to insert five stones consecutively from one side to perform the same function as the stick tool with the resulting multi-component construction. One Ara glaucogularis solved the task and innovated the stone construction after the experience with the stick tool. Two more subjects (one of each species) did so after having further functional experience of a single stone pushing a reward out of a shortened tube. These subjects were able to consistently solve the task, but often made errors, for example counter-productive stone insertions from the opposing end, even in some of the successful trials. Conversely, multiple trials without errors also suggested a strong goal direction. Their performance in the follow-up tasks was inconclusive since they sometimes inserted stones into un-baited or blocked 'dummy tubes', but this could have been an attention-deficit behaviour as subjects had not encountered these 'dummy tubes' before. Overall, the successful subjects' performance was so erratic that it proved difficult to conclude whether they had functional understanding of their multi-stone constructions.
| S-EPMC7979646 | biostudies-literature