scholarly journals Reconstructing the invasion route of DNA transposons using extant population samples

2019 ◽  
Author(s):  
Lukas Weilguny ◽  
Christos Vlachos ◽  
Divya Selvaraju ◽  
Robert Kofler
Keyword(s):  
P Element ◽  
Model Organisms ◽  
Migration Patterns ◽  
Dna Transposons ◽  
Time Points ◽  
Wide Range ◽  
Invasion Routes ◽  
Geographic Regions ◽  
Extant Population ◽  
Shed Light

AbstractReconstructing invasion routes of transposable elements (TEs), so far, required capturing an ongoing invasion with population samples from different geographic regions and time points. Here, we propose a more accessible approach. Abundantly occurring internal deletions of DNA transposons allow to trace the direction as well as the path of an invasion, even hundreds of generations after the spread of a TE. We validated this hypothesis with computer simulations and by accurately reproducing the route of the P-element invasion in Drosophila melanogaster. Finally, we used our method to shed light on the controversial hobo invasion in D. melanogaster. Our approach solely requires sequenced samples from extant populations and sequences of TEs of interest. Hence, DNA transposons in a wide range of model and non-model organisms may be analyzed. Our approach will further our understanding of TE dynamics, migration patterns, and the ecology of species.

scholarly journals Reconstructing the Invasion Route of the P-Element in Drosophila melanogaster Using Extant Population Samples

2020 ◽  
Vol 12 (11) ◽  
pp. 2139-2152
Author(s):  
Lukas Weilguny ◽  
Christos Vlachos ◽  
Divya Selvaraju ◽  
Robert Kofler
Keyword(s):  
Drosophila Melanogaster ◽  
P Element ◽  
High Rate ◽  
Reasonable Accuracy ◽  
Dna Transposons ◽  
African Populations ◽  
Spatially Distributed ◽  
Invasion Routes ◽  
Extant Population ◽  
European Populations

Abstract The P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.

scholarly journals The Berkeley Drosophila Genome Project Gene Disruption Project: Single P-Element Insertions Mutating 25% of Vital Drosophila Genes

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 135-177 ◽  
Author(s):  
Allan C Spradling ◽  
Dianne Stern ◽  
Amy Beaton ◽  
E Jay Rhem ◽  
Todd Laverty ◽  
...  
Keyword(s):  
Gene Disruption ◽  
Genome Project ◽  
Open Reading Frames ◽  
P Element ◽  
Model Organisms ◽  
Berkeley Drosophila Genome Project ◽  
Drosophila Genome ◽  
P Elements ◽  
Wide Range ◽  
Reading Frames

AbstractA fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking >920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing >250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring >85% of all Drosophila open reading frames under experimental control.

Sentence-Based Experience Logging in New Hearing Aid Users

2020 ◽  
Vol 29 (3S) ◽  
pp. 631-637
Author(s):  
Katja Lund ◽  
Rodrigo Ordoñez ◽  
Jens Bo Nielsen ◽  
Dorte Hammershøi
Keyword(s):  
Hearing Aid ◽  
Patient Experiences ◽  
Online Tool ◽  
Rehabilitation Process ◽  
Hearing Rehabilitation ◽  
Clinical Observations ◽  
Hearing Aid Use ◽  
Wide Range ◽  
Insight Into ◽  
Shed Light

Purpose The aim of this study was to develop a tool to gain insight into the daily experiences of new hearing aid users and to shed light on aspects of aided performance that may not be unveiled through standard questionnaires. Method The tool is developed based on clinical observations, patient experiences, expert involvement, and existing validated hearing rehabilitation questionnaires. Results An online tool for collecting data related to hearing aid use was developed. The tool is based on 453 prefabricated sentences representing experiences within 13 categories related to hearing aid use. Conclusions The tool has the potential to reflect a wide range of individual experiences with hearing aid use, including auditory and nonauditory aspects. These experiences may hold important knowledge for both the patient and the professional in the hearing rehabilitation process.

scholarly journals Adherence to Ketogenic and Mediterranean Study Diets in a Crossover Trial: The Keto–Med Randomized Trial

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 967
Author(s):  
Matthew J. Landry ◽  
Anthony Crimarco ◽  
Dalia Perelman ◽  
Lindsay R. Durand ◽  
Christina Petlura ◽  
...  
Keyword(s):  
Randomized Trial ◽  
Randomized Clinical Trials ◽  
Secondary Analysis ◽  
Critical Factor ◽  
Detailed Examination ◽  
Diet Patterns ◽  
Time Points ◽  
Study Results ◽  
Wide Range ◽  
Diet Pattern

Adherence is a critical factor to consider when interpreting study results from randomized clinical trials (RCTs) comparing one diet to another, but it is frequently not reported by researchers. The purpose of this secondary analysis of the Keto–Med randomized trial was to provide a detailed examination and comparison of the adherence to the two study diets (Well Formulated Ketogenic Diet (WFKD) and Mediterranean Plus (Med-Plus)) under the two conditions: all food being provided (delivered) and all food being obtained by individual participants (self-provided). Diet was assessed at six time points including baseline (x1), week 4 of each phase when participants were receiving food deliveries (x2), week 12 of each phase when participants were preparing and providing food on their own (x2), and 12 weeks after participants completed both diet phases and were free to choose their own diet pattern (x1). The adherence scores for WFKD and Med-Plus were developed specifically for this study. Average adherence to the two diet patterns was very similar during both on-study time points of the intervention. Throughout the study, a wide range of adherence was observed among participants—for both diet types and during both the delivery phase and self-provided phase. Insight from this assessment of adherence may aid other researchers when answering the important question of how to improve behavioral adherence during dietary trials. This study is registered at clinicaltrials.gov NCT03810378.

scholarly journals mtDNAcombine: tools to combine sequences from multiple studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica
Keyword(s):  
Sequence Data ◽  
Data Extraction ◽  
Bayesian Skyline Plot ◽  
Model Organisms ◽  
Data Sets ◽  
Data Handling ◽  
Online Database ◽  
Genetic Studies ◽  
Wide Range ◽  
Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

scholarly journals An In Vitro Cell Culture Model for Pyoverdine-Mediated Virulence

Pathogens ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 9
Author(s):  
Donghoon Kang ◽  
Natalia V. Kirienko
Keyword(s):  
Cell Culture ◽  
Virulence Factors ◽  
Model Organisms ◽  
Cell Culture Model ◽  
Chronic Infections ◽  
In Vitro Cell Culture ◽  
Mitochondrial Homeostasis ◽  
Culture Model ◽  
Wide Range

Pseudomonas aeruginosa is a multidrug-resistant, opportunistic pathogen that utilizes a wide-range of virulence factors to cause acute, life-threatening infections in immunocompromised patients, especially those in intensive care units. It also causes debilitating chronic infections that shorten lives and worsen the quality of life for cystic fibrosis patients. One of the key virulence factors in P. aeruginosa is the siderophore pyoverdine, which provides the pathogen with iron during infection, regulates the production of secreted toxins, and disrupts host iron and mitochondrial homeostasis. These roles have been characterized in model organisms such as Caenorhabditis elegans and mice. However, an intermediary system, using cell culture to investigate the activity of this siderophore has been absent. In this report, we describe such a system, using murine macrophages treated with pyoverdine. We demonstrate that pyoverdine-rich filtrates from P. aeruginosa exhibit substantial cytotoxicity, and that the inhibition of pyoverdine production (genetic or chemical) is sufficient to mitigate virulence. Furthermore, consistent with previous observations made in C. elegans, pyoverdine translocates into cells and disrupts host mitochondrial homeostasis. Most importantly, we observe a strong correlation between pyoverdine production and virulence in P. aeruginosa clinical isolates, confirming pyoverdine’s value as a promising target for therapeutic intervention. This in vitro cell culture model will allow rapid validation of pyoverdine antivirulents in a simple but physiologically relevant manner.

scholarly journals Beyond cultural and geographical proximity: delving into the factors that influence the dynamics of academic relationships between students in higher education

2021 ◽  
Author(s):  
José-Vicente Tomás-Miquel ◽  
Jordi Capó-Vicedo
Keyword(s):  
University Students ◽  
Academic Research ◽  
Past Research ◽  
Academic Networks ◽  
Level Data ◽  
Wide Range ◽  
Specific Stage ◽  
The University ◽  
Proximity Dimensions ◽  
Shed Light

AbstractScholars have widely recognised the importance of academic relationships between students at the university. While much of the past research has focused on studying their influence on different aspects such as the students’ academic performance or their emotional stability, less is known about their dynamics and the factors that influence the formation and dissolution of linkages between university students in academic networks. In this paper, we try to shed light on this issue by exploring through stochastic actor-oriented models and student-level data the influence that a set of proximity factors may have on formation of these relationships over the entire period in which students are enrolled at the university. Our findings confirm that the establishment of academic relationships is derived, in part, from a wide range of proximity dimensions of a social, personal, geographical, cultural and academic nature. Furthermore, and unlike previous studies, this research also empirically confirms that the specific stage in which the student is at the university determines the influence of these proximity factors on the dynamics of academic relationships. In this regard, beyond cultural and geographic proximities that only influence the first years at the university, students shape their relationships as they progress in their studies from similarities in more strategic aspects such as academic and personal closeness. These results may have significant implications for both academic research and university policies.

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

scholarly journals Messianism, rationalism and inter-Asian connections: The Majalis-i Jahangiri (1608–11) and the socio-intellectual history of the Mughal ‘ulama

2017 ◽  
Vol 54 (3) ◽  
pp. 317-338 ◽  
Author(s):  
Corinne Lefèvre
Keyword(s):  
Central Asia ◽  
Intellectual History ◽  
State Building ◽  
Specific Role ◽  
Wide Range ◽  
History Of ◽  
Muslim Intellectuals ◽  
Shed Light

Relying on the Majalis-i Jahangiri (1608–11) by ʿAbd al-Sattar b. Qasim Lahauri, this essay explores some of the discussions the Mughal Emperor Jahangir (r. 1605–27) conducted with a wide range of scholars, from Brahmans and ʿulama to Jesuit padres and Jewish savants. By far the most numerous, the debates bearing on Islam and involving Muslim intellectuals are especially significant on several accounts. First, because they illuminate how, following in the steps of his father Akbar (r. 1556–605), Jahangir was able to conciliate his messianic claims with a strong engagement with reason and to turn this combination into a formidable instrument for confession and state building. These conversations also provide promising avenues to think afresh the socio-intellectual history of the Mughal ʿulama inasmuch as they capture the challenges and adjustments attendant on imperial patronage, depict the jockeying for influence and positions among intellectuals (particularly between Indo-Muslim and Iranian lettrés), and shed light on relatively little known figures or on unexplored facets of more prominent individuals. In addition, the specific role played by scholars hailing from Iran—and, to a lesser extent, from Central Asia—in the juridical-religious disputes of the Indian court shows how crucial inter-Asian connections and networks were in the fashioning of Mughal ideology but also the ways in which the ongoing flow of émigré ʿulama was disciplined before being incorporated into the empire.

scholarly journals Monitoring Radiotherapeutic Response in Prostate Cancer Patients Using High Throughput FTIR Spectroscopy of Liquid Biopsies

Cancers ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 925 ◽  
Author(s):  
Dinesh K.R. Medipally ◽  
Thi Nguyet Que Nguyen ◽  
Jane Bryant ◽  
Valérie Untereiner ◽  
Ganesh D. Sockalingum ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Blood Plasma ◽  
Ftir Spectroscopy ◽  
Cancer Patients ◽  
Radiation Toxicity ◽  
Plasma Samples ◽  
Analysis Model ◽  
Liquid Biopsies ◽  
Time Points ◽  
Wide Range

Radiation therapy (RT) is used to treat approximately 50% of all cancer patients. However, RT causes a wide range of adverse late effects that can affect a patient’s quality of life. There are currently no predictive assays in clinical use to identify patients at risk of normal tissue radiation toxicity. This study aimed to investigate the potential of Fourier transform infrared (FTIR) spectroscopy for monitoring radiotherapeutic response. Blood plasma was acquired from 53 prostate cancer patients at five different time points: prior to treatment, after hormone treatment, at the end of radiotherapy, two months post radiotherapy and eight months post radiotherapy. FTIR spectra were recorded from plasma samples at all time points and the data was analysed using MATLAB software. Discrimination was observed between spectra recorded at baseline versus follow up time points, as well as between spectra from patients showing minimal and severe acute and late toxicity using principal component analysis. A partial least squares discriminant analysis model achieved sensitivity and specificity rates ranging from 80% to 99%. This technology may have potential to monitor radiotherapeutic response in prostate cancer patients using non-invasive blood plasma samples and could lead to individualised patient radiotherapy.

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