Výsledky vyhledávání - "John M. Urban"

Akademický článek

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

Autor: John M. Urban, Michael S. Foulk, Jacob E. Bliss, C. Michelle Coleman, Nanyan Lu, Reza Mazloom, Susan J. Brown, Allan C. Spradling, Susan A. Gerbi

Publikováno v: BMC Genomics, Vol 22, Iss 1, Pp 1-23 (2021)

Abstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisj

Externí odkaz: https://doaj.org/article/dc3a54e02e7144beacef28bd220d2a9e

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Akademický článek

MinION Analysis and Reference Consortium: Phase 1 data release and analysis [version 1; referees: 2 approved]

Publikováno v: F1000Research, Vol 4 (2015)

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologie

Externí odkaz: https://doaj.org/article/b9fd4c6fe9d440deaa166902e0f8d188

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Akademický článek

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells

Autor: Liang-Yu Pang, Steven DeLuca, Haolong Zhu, John M Urban, Allan C Spradling

Publikováno v: eLife, Vol 12 (2023)

Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSCs) perpetuate without change over evolutionary time and generate

Externí odkaz: https://doaj.org/article/9157b37e1c454bf6bae501445ff206fc

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Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods

Autor: Robert B. Baird, John M. Urban, Andrew J. Mongue, Kamil S. Jaron, Christina N. Hodson, Malte Grewoldt, Simon H. Martin, Laura Ross

Publikováno v: Baird, R B, Urban, J M, Mongue, A J, Jaron, K S, Hodson, C N, Grewoldt, M, Martin, S H & Ross, L 2023, ' Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods ', Molecular Biology and Evolution . https://doi.org/10.1093/molbev/msad148
Baird, R B, Urban, J M, Mongue, A J, Jaron, K S, Hodson, C N, Grewoldt, M, Martin, S H & Ross, L 2023, ' Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods ', Molecular Biology and Evolution, vol. 40, no. 7, msad148 . https://doi.org/10.1093/molbev/msad148

Sex determination is a key developmental process, yet it is remarkably variable across the tree of life. The dipteran family Sciaridae exhibits one of the most unusual sex determination systems in which mothers control offspring sex through selective

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a5ec5232dc5b686936574e96ccddd5a
https://pure.au.dk/portal/da/publications/recent-evolution-of-a-maternallyacting-sexdetermining-supergene-in-a-fly-with-singlesex-broods(da7a2a0a-d4fb-40c5-b6d6-585998264a41).html

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Chromosome-scale scaffolding of the fungus gnat genome (Diptera:Bradysia coprophila)

Autor: John M. Urban, Susan A. Gerbi, Allan C. Spradling

BackgroundThe lower dipteran fungus gnat,Bradysia(Sciara)coprophila, has unusual chromosome biology. Chromosome imprinting was first discovered in this system. All paternal chromosomes are eliminated during spermatogenesis whereas both maternal X sis

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::7b7c6b9c7cc9a478bd23753016527346
https://doi.org/10.1101/2022.11.03.515061

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Sciara coprophila larvae upregulate DNA repair pathways and downregulate developmental regulators in response to ionizing radiation

Autor: Jack R. Bateman, Julia Borden, Alexia Brown, Jaison Jain, Jacob E. Bliss, Bethany J. Thach, Kodie R. Garza, Susan A. Gerbi, John M. Urban

Robust DNA damage prevention and repair strategies are crucial to faithful reproduction and inheritance of the genetic material. Although many molecular pathways that respond to DNA damage are well conserved through evolution, the quality and effecti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ef9c3ae79b81eb825f7bdf3ea12d93bd
https://doi.org/10.1101/2021.10.28.466123

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High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

Autor: Jacob E. Bliss, Susan A. Gerbi, Nanyan Lu, John M. Urban, Reza Mazloom, C Michelle Coleman, Michael S. Foulk, Susan J. Brown, Allan C. Spradling

Publikováno v: BMC Genomics, Vol 22, Iss 1, Pp 1-23 (2021)
BMC Genomics

Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9a18119d638e1fcd55b8bb37f4ccf6a
https://doi.org/10.1186/s12864-021-07926-2

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Single-molecule sequencing of long DNA molecules allows high contiguityde novogenome assembly for the fungus fly,Sciara coprophila

Autor: Susan A. Gerbi, Nanyan Lu, John M. Urban, Jacob E. Bliss, C. M. Coleman, Michael S. Foulk, Reza Mazloom, Susan J. Brown, Allan C. Spradling

The lower Dipteran fungus fly,Sciara coprophila, has many unique biological features. For example,Sciaraundergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b8c07ceb9cd753307997dd7b650019d4
https://doi.org/10.1101/2020.02.24.963009

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Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

Autor: John M. Urban, Susan A. Gerbi, Michael S. Foulk, Cinzia Casella

Publikováno v: Foulk, M S, Urban, J M, Casella, C & Gerbi, S A 2015, ' Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins ', Genome Research, vol. 25, no. 5, pp. 725-735 . https://doi.org/10.1101/gr.183848.114

Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA w

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3b75cf9807facf62fc24ddbace600acb
https://doi.org/10.1101/gr.183848.114

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The Drosophila CLAMP protein associates with diverse proteins on chromatin

Autor: Erica Larschan, John M. Urban, Guray Kuzu, Jennifer A. Urban

Publikováno v: PLoS ONE
PLoS ONE, Vol 12, Iss 12, p e0189772 (2017)

Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4f7edf289b42d2a7e73e26dde6f933a
https://pubmed.ncbi.nlm.nih.gov/29281702

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