scholarly journals Pengembangan Modul Genetika Berbasis Praktikum Proyek Memanfaatkan Drosophila melanogaster Pada Topik Regulasi Ekspresi Gen Eukariot

2018 ◽  
Vol 6 (02) ◽  
pp. 140-154
Author(s):  
Shefa Dwijayanti Ramadani
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Student Assessment ◽  
Regulation Of Gene Expression ◽  
Resource Development ◽  
Learning Resource ◽  
Concept Understanding ◽  
Practical Activity ◽  
Module Design ◽  
Learning Module

Ideal learning should encourage students to be actively involved, both physically and mentally during the learning process. Unfortunately, Genetics lectures at higher education were still widely implemented conventionally through theoretical studies without involving practical activities. This condition was at least caused by two factors: (1) practical activity wasn’t designed in the curriculum, so it had never been done and (2) there weren’t enough learning resources available to encourage the students to carry out practical activity independently. The development of learning module that utilize Drosophila melanogaster was expected to enhance student’s activity and concept understanding on the topic of regulation of gene expression in eukaryotes. ADDIE was  used as instructional module design, while the instrument used include observation sheets, student assessment sheets, and module validation sheets by Genetic experts and learning resource development experts. The results showed that the percentage of assessment based on small group trial was 90.8%; while validation results by Genetic and learning resource development expert were 92.2% and 92.5%, respectively. This means that the learning module was valid with very good qualification. Thus, the regulation of gene expression module can be used by students to obtain concept understanding more easily, as well as facilitating the students to empower skills and scientific values. Keywords: Project Practicum, Drosophila Melanogaster, Development of Module, Regulation of Gene Expression Abstrak Pembelajaran ideal adalah pembelajaran yang mampu mendorong siswa untuk terlibat secara aktif, baik secara mental maupun fisik selama proses pembelajaran. Sayangnya, perkuliahan Genetika di Perguruan Tinggi masih banyak dilaksanakan secara konvensional melalui kajian teoritis tanpa melibatkan aktivitas praktikum. Kondisi ini setidaknya disebabkan oleh dua faktor yaitu: (1) aktivitas praktikum memang tidak dirancang dalam kurikulum, sehingga belum pernah dilakukan dan (2) belum tersedia sumber belajar yang cukup untuk mendorong mahasiswa melaksanakan kegiatan praktikum secara mandiri. Pengembangan modul pembelajaran yang memanfaatkan Drosophila melanogaster diharapkan dapat mendorong aktivitas maupun pemahaman konsep mahasiswa pada topik regulasi ekspresi gen pada eukariot. ADDIE digunakan sebagai desain modul pembelajaran, sementara instrumen yang digunakan meliputi lembar observasi, lembar penilaian/respons mahasiswa, dan lembar validasi modul oleh ahli Genetika dan ahli pengembangan bahan ajar. Hasil penelitian menunjukkan bahwa persentase penilaian berdasarkan uji coba kelompok kecil sebesar 90,8%;  sementara hasil validasi oleh ahli materi dan ahli pengembangan bahan ajar masing-masing sebesar 92,2% dan 92,5%.  Hal ini berarti bahwa modul dinilai layak dengan kualifikasi sangat baik. Dengan demikian, modul regulasi ekspresi gen dapat digunakan oleh mahasiswa untuk memperoleh pemahaman konsep secara lebih mudah sekaligus memfasilitasi mahasiswa untuk memberdayakan keterampilan dan sifat-sifat ilmiah.

scholarly journals Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190341 ◽  
Author(s):  
Judit Salces-Ortiz ◽  
Carlos Vargas-Chavez ◽  
Lain Guio ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Organophosphate Insecticide ◽  
Single Nucleotide ◽  
Insecticide Exposure ◽  
Genomic Response

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis -regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

scholarly journals Regulation of gene expression is preserved in aging Drosophila melanogaster

1998 ◽  
Vol 8 (8) ◽  
pp. 475-478 ◽  
Author(s):  
Blanka Rogina ◽  
James W. Vaupel ◽  
Linda Partridge ◽  
Stephen L. Helfand
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Regulation Of Gene Expression

scholarly journals Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster

2021 ◽  
Vol 11 (4) ◽  
pp. 20200076 ◽  
Author(s):  
Leandro Murgas ◽  
Sebastian Contreras-Riquelme ◽  
J. Eduardo Martínez-Hernandez ◽  
Camilo Villaman ◽  
Rodrigo Santibáñez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Reference Network ◽  
Specific Gene ◽  
Gene Regulatory ◽  
Context Specific

The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster . Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io .

scholarly journals Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

2021 ◽  
Author(s):  
Ashley R Albright ◽  
Michael R Stadler ◽  
Michael Eisen
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Rna Sequencing ◽  
Regulation Of Gene Expression ◽  
Single Nucleus ◽  
Differential Gene ◽  
The Difference ◽  
In Situ Hybridizations ◽  
Genome Activation

Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the practicality of single-nucleus RNA sequencing in the context of a real biological question, here we look at the difference in gene expression between control and an insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we present multiple examples of differential gene expression between control and maternal CTCF null nuclei in one or more clusters, but not in bulk when grouping expression across all nuclei. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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