scholarly journals REMI-seq: Development of methods and resources for functional genomics inDictyostelium

2019 ◽  
Author(s):  
Nicole Gruenheit ◽  
Amy Baldwin ◽  
Balint Stewart ◽  
Sarah Jaques ◽  
Thomas Keller ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Large Scale ◽  
Model System ◽  
Step Change ◽  
Model Systems ◽  
Social Amoeba ◽  
Genome Wide ◽  
The Social ◽  
Higher Eukaryotes ◽  
Eukaryotic Microbe

AbstractGenomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoebaDictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in cell, developmental and evolutionary biology. However, its utility is hampered by the inefficiency with which sequence, transcriptome or proteome variation can be linked to phenotype. To address this, we have developed methods (REMI-seq) to (1) generate a near genome-wide resource of individual mutants (2) allow large-scale parallel phenotyping. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Therefore, these methods and resources provide a step change for high throughput gene discovery in a key model system, and the study of genes affecting traits associated with higher eukaryotes.

scholarly journals Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Nicole Gruenheit ◽  
Amy Baldwin ◽  
Balint Stewart ◽  
Sarah Jaques ◽  
Thomas Keller ◽  
...  
Keyword(s):  
Dictyostelium Discoideum ◽  
High Throughput ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Function Analysis ◽  
Model Systems ◽  
Genome Wide ◽  
The Social ◽  
Drug Resistance Marker

Abstract Background Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.

scholarly journals Microbe Profile: Dictyostelium discoideum: model system for development, chemotaxis and biomedical research

Microbiology ◽  
2021 ◽  
Author(s):  
Catherine J. Pears ◽  
Julian D. Gross
Keyword(s):  
Pattern Formation ◽  
Cell Motility ◽  
Dictyostelium Discoideum ◽  
Biomedical Research ◽  
Model System ◽  
Developmental Pattern ◽  
Social Amoeba ◽  
The Social ◽  
Host Pathogen ◽  
Soil Amoeba

The social amoeba Dictyostelium discoideum is a versatile organism that is unusual in alternating between single-celled and multi-celled forms. It possesses highly-developed systems for cell motility and chemotaxis, phagocytosis, and developmental pattern formation. As a soil amoeba growing on microorganisms, it is exposed to many potential pathogens; it thus provides fruitful ways of investigating host-pathogen interactions and is emerging as an influential model for biomedical research.

scholarly journals BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

2021 ◽  
Vol 7 (2) ◽  
Author(s):  
Adrian Sven Geissler ◽  
Christian Anthon ◽  
Ferhat Alkan ◽  
Enrique González-Tortuero ◽  
Line Dahl Poulsen ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Type Species ◽  
Large Scale ◽  
Information Access ◽  
Model Systems ◽  
Transcription Start ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Transcript Map

A large part of our current understanding of gene regulation in Gram-positive bacteria is based on Bacillus subtilis , as it is one of the most well studied bacterial model systems. The rapid growth in data concerning its molecular and genomic biology is distributed across multiple annotation resources. Consequently, the interpretation of data from further B. subtilis experiments becomes increasingly challenging in both low- and large-scale analyses. Additionally, B. subtilis annotation of structured RNA and non-coding RNA (ncRNA), as well as the operon structure, is still lagging behind the annotation of the coding sequences. To address these challenges, we created the B. subtilis genome atlas, BSGatlas, which integrates and unifies multiple existing annotation resources. Compared to any of the individual resources, the BSGatlas contains twice as many ncRNAs, while improving the positional annotation for 70 % of the ncRNAs. Furthermore, we combined known transcription start and termination sites with lists of known co-transcribed gene sets to create a comprehensive transcript map. The combination with transcription start/termination site annotations resulted in 717 new sets of co-transcribed genes and 5335 untranslated regions (UTRs). In comparison to existing resources, the number of 5′ and 3′ UTRs increased nearly fivefold, and the number of internal UTRs doubled. The transcript map is organized in 2266 operons, which provides transcriptional annotation for 92 % of all genes in the genome compared to the at most 82 % by previous resources. We predicted an off-target-aware genome-wide library of CRISPR–Cas9 guide RNAs, which we also linked to polycistronic operons. We provide the BSGatlas in multiple forms: as a website (https://rth.dk/resources/bsgatlas/), an annotation hub for display in the UCSC genome browser, supplementary tables and standardized GFF3 format, which can be used in large scale -omics studies. By complementing existing resources, the BSGatlas supports analyses of the B. subtilis genome and its molecular biology with respect to not only non-coding genes but also genome-wide transcriptional relationships of all genes.

Model systems of genetically modified platelets

Blood ◽  
2012 ◽  
Vol 119 (7) ◽  
pp. 1634-1642 ◽  
Author(s):  
Tim Thijs ◽  
Hans Deckmyn ◽  
Katleen Broos
Keyword(s):  
Animal Models ◽  
Large Scale ◽  
Genetically Modified ◽  
Model Systems ◽  
Screening Programs ◽  
Genome Wide ◽  
Increasing Demand ◽  
Improved Model ◽  
Large Scale Screening

Abstract Although platelets are the smallest cells in the blood, they are implied in various processes ranging from immunology and oncology to thrombosis and hemostasis. Many large-scale screening programs, genome-wide association, and “omics” studies have generated lists of genes and loci that are probably involved in the formation or physiology of platelets under normal and pathologic conditions. This creates an increasing demand for new and improved model systems that allow functional assessment of the corresponding gene products in vivo. Such animal models not only render invaluable insight in the platelet biology, but in addition, provide improved test systems for the validation of newly developed anti-thrombotics. This review summarizes the most important models to generate transgenic platelets and to study their influence on platelet physiology in vivo. Here we focus on the zebrafish morpholino oligonucleotide technology, the (platelet-specific) knockout mouse, and the transplantation of genetically modified human or murine platelet progenitor cells in myelo-conditioned mice. The various strengths and pitfalls of these animal models are illustrated by recent examples from the platelet field. Finally, we highlight the latest developments in genetic engineering techniques and their possible application in platelet research.

Multiple-source Record Linkage in a Rural Industrial Community, 1680–1820

1994 ◽  
Vol 6 (3) ◽  
pp. 133-142 ◽  
Author(s):  
Steve King
Keyword(s):  
Early Modern ◽  
Large Scale ◽  
Social Economic ◽  
Life Cycles ◽  
Multiple Source ◽  
Demographic Analysis ◽  
Ordinary People ◽  
Industrial Community ◽  
The Social ◽  
Broad Outline

Re-creating the social, economic and demographic life-cycles of ordinary people is one way in which historians might engage with the complex continuities and changes which underlay the development of early modern communities. Little, however, has been written on the ways in which historians might deploy computers, rather than card indexes, to the task of identifying such life cycles from the jumble of the sources generated by local and national administration. This article suggests that multiple-source linkage is central to historical and demographic analysis, and reviews, in broad outline, some of the procedures adopted in a study which aims at large scale life cycle reconstruction.

Bologna, My Love: Il Cinema Ritrovato

2019 ◽  
Vol 73 (2) ◽  
pp. 72-79
Author(s):  
Carla Marcantonio
Keyword(s):  
Social Justice ◽  
Fairy Tale ◽  
Large Scale ◽  
Francis Ford Coppola ◽  
The Social ◽  
Ongoing Project

FQ books editor Carla Marcantonio guides readers through the 33rd edition of Il Cinema Ritrovato Festival held each year in Bologna at the end of June. Highlights of this year's festival included a restoration of one of Vittorio De Sica's hard-to-find and hence lesser-known films, the social justice fairy tale, Miracolo a Milano (Miracle in Milan, 1951). The film was presented by De Sica's daughter, Emi De Sica, and was an example of the ongoing project to restore De Sica's archive, which was given to the Cineteca de Bologna in 2016. Marcantonio also notes her unexpected responses to certain reviewings; Apocalypse Now: Final Cut (2019), presented by Francis Ford Coppola on the large-scale screen of Piazza Maggiore and accompanied by remastered Dolby Atmos sound, struck her as a tour-de-force while a restoration of David Lynch's Blue Velvet (1986) had lost some of its strange allure.

KETERTINDASAN MELAYU DALAM CERPEN “SUKU POMPONG” KARYA FEDLI AZIS DAN CERPEN “RUMAH DI UJUNG KAMPUNG” KARYA HANG KAFRAWI

2017 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Marlina Marlina
Keyword(s):  
Short Stories ◽  
Large Scale ◽  
Social Aspects ◽  
Land Conversion ◽  
The Public ◽  
Historical Reality ◽  
Sociological Approach ◽  
The Social ◽  
Imaginative Literature ◽  
The Village

Reading short stories “Suku Pompong” (Pompong Tribe) and “Rumah di Ujung Kampung” (House at the End of the Village) is like reading a historical reality that is happening on the ground of Riau Malay. The exploitation of forest resources on a large scale in recent decades in Riau Province has changed the land use of the area of intact forest into plantation area. The exploitation process causes friction in the community. The friction is eventually lead to conflict between communities and plantation companies. Their struggle to resolve conflicts and maintain their ancestral land, the strength of the company that has the license to the land and sadness when the public finally has always been on the losing side. This study objected to describe the objective reality of the Malay community in terms of land conversion, the communal land into plantations and reality of imaginative literature contained in the short stories “Suku Pompong” dan “Rumah di Ujung Kampung”. This study applied the sociology of literature approach, while the sociological approach to literature is a literary approach that specializes in reviewing literature by considering the social aspects. Based on these approaches, it can be concluded that short stories Suku Pompong and Rumah di Ujung Jalan are short stories that raised the reality of the Malay community.AbstrakMembaca cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung” seperti membaca sebuah realita sejarah yang terjadi di tanah Melayu Riau. Ekploitasi sumber daya hutan secara besar-besaran pada beberapa dekade terakhir di Provinsi Riau telah mengubah tata guna lahan dari kawasan hutan yang utuh menjadi kawasan perkebunan. Proses eksploitasi tersebut menimbulkan gesekan-gesekan dalam masyarakat. Gesekan-gesekan inilah yang akhirnya menimbulkan konflik antara masyarakat dengan pihak perusahaan perkebunan. Perjuangan masyarakat dalam menyelesaikan konflik dan mempertahankan tanah leluhur mereka, kekuatan pihak perusahaan yang memiliki surat izin atas tanah tersebut, dan kesedihan ketika masyarakat akhirnya selalu berada di pihak yang kalah. Penelitian ini bertujuan untuk mendeskripsikan realitas objektif masyarakat Melayu Riau dalam hal alih fungsi lahan, dari lahan tanah ulayat menjadi lahan perkebunan, dan realititas imajinatif sastra yang terdapat dalam cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung”. Penelitian ini menggunakan pendekatan sosiologi sastra, yaitu suatu pendekatan sastra yang mengkhususkan diri dalam menelaah karya sastra dengan mempertimbangkan segi-segi sosial kemasyarakatan. Dari pendekatan tersebut dapat diambil kesimpulan bahwa cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung” memang merupakan cerpen yang mengangkat realitas masyarakat Melayu Riau.

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