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  1. Article: The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in

    Dubey, Shiv Mani / Han, Soeun / Stutzman, Nathan / Prigge, Michael J / Medvecká, Eva / Platre, Matthieu Pierre / Busch, Wolfgang / Fendrych, Matyáš / Estelle, Mark

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this ... ...

    Abstract The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, are essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response while it regulates rapid changes in cell growth that contribute to root gravitropism.
    Language English
    Publishing date 2023-01-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.04.522696
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development.

    Zhang, Tao / Noll, Sarah E / Peng, Jesus T / Klair, Amman / Tripka, Abigail / Stutzman, Nathan / Cheng, Casey / Zare, Richard N / Dickinson, Alexandra J

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2567

    Abstract: Understanding how plants grow is critical for agriculture and fundamental for illuminating principles of multicellular development. Here, we apply desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to the chemical mapping of the ... ...

    Abstract Understanding how plants grow is critical for agriculture and fundamental for illuminating principles of multicellular development. Here, we apply desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to the chemical mapping of the developing maize root. This technique reveals a range of small molecule distribution patterns across the gradient of stem cell differentiation in the root. To understand the developmental logic of these patterns, we examine tricarboxylic acid (TCA) cycle metabolites. In both Arabidopsis and maize, we find evidence that elements of the TCA cycle are enriched in developmentally opposing regions. We find that these metabolites, particularly succinate, aconitate, citrate, and α-ketoglutarate, control root development in diverse and distinct ways. Critically, the developmental effects of certain TCA metabolites on stem cell behavior do not correlate with changes in ATP production. These results present insights into development and suggest practical means for controlling plant growth.
    MeSH term(s) Tricarboxylic Acids ; Spectrometry, Mass, Electrospray Ionization/methods ; Citric Acid Cycle ; Diagnostic Imaging ; Growth and Development
    Chemical Substances Tricarboxylic Acids
    Language English
    Publishing date 2023-05-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-38150-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana.

    Dubey, Shiv Mani / Han, Soeun / Stutzman, Nathan / Prigge, Michael J / Medvecká, Eva / Platre, Matthieu Pierre / Busch, Wolfgang / Fendrych, Matyáš / Estelle, Mark

    Molecular plant

    2023  Volume 16, Issue 7, Page(s) 1120–1130

    Abstract: The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this ... ...

    Abstract The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, is essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition by auxin. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx, which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response, whereas it regulates rapid changes in cell growth that contribute to root gravitropism.
    MeSH term(s) Arabidopsis/metabolism ; Indoleacetic Acids/pharmacology ; Indoleacetic Acids/metabolism ; Arabidopsis Proteins/metabolism ; F-Box Proteins/metabolism ; Plant Roots/metabolism ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/metabolism ; Plant Growth Regulators/metabolism ; Cytosol/metabolism ; Gene Expression Regulation, Plant
    Chemical Substances Indoleacetic Acids ; Arabidopsis Proteins ; F-Box Proteins ; Receptors, Cell Surface ; Plant Growth Regulators
    Language English
    Publishing date 2023-06-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2393618-6
    ISSN 1752-9867 ; 1674-2052
    ISSN (online) 1752-9867
    ISSN 1674-2052
    DOI 10.1016/j.molp.2023.06.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana

    Dubey, Shiv Mani / Han, Soeun / Stutzman, Nathan / Prigge, Michael J. / Medvecká, Eva / Platre, Matthieu Pierre / Busch, Wolfgang / Fendrych, Matyáš / Estelle, Mark

    Molecular Plant. 2023 July, v. 16, no. 7 p.1120-1130

    2023  

    Abstract: The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this ... ...

    Abstract The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, is essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition by auxin. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx, which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response, whereas it regulates rapid changes in cell growth that contribute to root gravitropism.
    Keywords Arabidopsis thaliana ; auxins ; calcium ; cell growth ; gravitropism ; growth retardation ; lateral roots ; plant hormones ; root growth ; transcription (genetics) ; auxin signaling ; Arabidopsis ; lateral root
    Language English
    Dates of publication 2023-07
    Size p. 1120-1130.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 2393618-6
    ISSN 1752-9867 ; 1674-2052
    ISSN (online) 1752-9867
    ISSN 1674-2052
    DOI 10.1016/j.molp.2023.06.008
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience.

    Evans, Cory J / Olson, John M / Mondal, Bama Charan / Kandimalla, Pratyush / Abbasi, Ariano / Abdusamad, Mai M / Acosta, Osvaldo / Ainsworth, Julia A / Akram, Haris M / Albert, Ralph B / Alegria-Leal, Elitzander / Alexander, Kai Y / Ayala, Angelica C / Balashova, Nataliya S / Barber, Rebecca M / Bassi, Harmanjit / Bennion, Sean P / Beyder, Miriam / Bhatt, Kush V /
    Bhoot, Chinmay / Bradshaw, Aaron W / Brannigan, Tierney G / Cao, Boyu / Cashell, Yancey Y / Chai, Timothy / Chan, Alex W / Chan, Carissa / Chang, Inho / Chang, Jonathan / Chang, Michael T / Chang, Patrick W / Chang, Stephen / Chari, Neel / Chassiakos, Alexander J / Chen, Iris E / Chen, Vivian K / Chen, Zheying / Cheng, Marsha R / Chiang, Mimi / Chiu, Vivian / Choi, Sharon / Chung, Jun Ho / Contreras, Liset / Corona, Edgar / Cruz, Courtney J / Cruz, Renae L / Dang, Jefferson M / Dasari, Suhas P / De La Fuente, Justin R O / Del Rio, Oscar M A / Dennis, Emily R / Dertsakyan, Petros S / Dey, Ipsita / Distler, Rachel S / Dong, Zhiqiao / Dorman, Leah C / Douglass, Mark A / Ehresman, Allysen B / Fu, Ivy H / Fua, Andrea / Full, Sean M / Ghaffari-Rafi, Arash / Ghani, Asmar Abdul / Giap, Bosco / Gill, Sonia / Gill, Zafar S / Gills, Nicholas J / Godavarthi, Sindhuja / Golnazarian, Talin / Goyal, Raghav / Gray, Ricardo / Grunfeld, Alexander M / Gu, Kelly M / Gutierrez, Natalia C / Ha, An N / Hamid, Iman / Hanson, Ashley / Hao, Celesti / He, Chongbin / He, Mengshi / Hedtke, Joshua P / Hernandez, Ysrael K / Hlaing, Hnin / Hobby, Faith A / Hoi, Karen / Hope, Ashley C / Hosseinian, Sahra M / Hsu, Alice / Hsueh, Jennifer / Hu, Eileen / Hu, Spencer S / Huang, Stephanie / Huang, Wilson / Huynh, Melanie / Javier, Carmen / Jeon, Na Eun / Ji, Sunjong / Johal, Jasmin / John, Amala / Johnson, Lauren / Kadakia, Saurin / Kakade, Namrata / Kamel, Sarah / Kaur, Ravinder / Khatra, Jagteshwar S / Kho, Jeffrey A / Kim, Caleb / Kim, Emily Jin-Kyung / Kim, Hee Jong / Kim, Hyun Wook / Kim, Jin Hee / Kim, Seong Ah / Kim, Woo Kyeom / Kit, Brian / La, Cindy / Lai, Jonathan / Lam, Vivian / Le, Nguyen Khoi / Lee, Chi Ju / Lee, Dana / Lee, Dong Yeon / Lee, James / Lee, Jason / Lee, Jessica / Lee, Ju-Yeon / Lee, Sharon / Lee, Terrence C / Lee, Victoria / Li, Amber J / Li, Jialing / Libro, Alexandra M / Lien, Irvin C / Lim, Mia / Lin, Jeffrey M / Liu, Connie Y / Liu, Steven C / Louie, Irene / Lu, Shijia W / Luo, William Y / Luu, Tiffany / Madrigal, Josef T / Mai, Yishan / Miya, Darron I / Mohammadi, Mina / Mohanta, Sayonika / Mokwena, Tebogo / Montoya, Tonatiuh / Mould, Dallas L / Murata, Mark R / Muthaiya, Janani / Naicker, Seethim / Neebe, Mallory R / Ngo, Amy / Ngo, Duy Q / Ngo, Jamie A / Nguyen, Anh T / Nguyen, Huy C X / Nguyen, Rina H / Nguyen, Thao T T / Nguyen, Vincent T / Nishida, Kevin / Oh, Seo-Kyung / Omi, Kristen M / Onglatco, Mary C / Almazan, Guadalupe Ortega / Paguntalan, Jahzeel / Panchal, Maharshi / Pang, Stephanie / Parikh, Harin B / Patel, Purvi D / Patel, Trisha H / Petersen, Julia E / Pham, Steven / Phan-Everson, Tien M / Pokhriyal, Megha / Popovich, Davis W / Quaal, Adam T / Querubin, Karl / Resendiz, Anabel / Riabkova, Nadezhda / Rong, Fred / Salarkia, Sarah / Sama, Nateli / Sang, Elaine / Sanville, David A / Schoen, Emily R / Shen, Zhouyang / Siangchin, Ken / Sibal, Gabrielle / Sin, Garuem / Sjarif, Jasmine / Smith, Christopher J / Soeboer, Annisa N / Sosa, Cristian / Spitters, Derek / Stender, Bryan / Su, Chloe C / Summapund, Jenny / Sun, Beatrice J / Sutanto, Christine / Tan, Jaime S / Tan, Nguon L / Tangmatitam, Parich / Trac, Cindy K / Tran, Conny / Tran, Daniel / Tran, Duy / Tran, Vina / Truong, Patrick A / Tsai, Brandon L / Tsai, Pei-Hua / Tsui, C Kimberly / Uriu, Jackson K / Venkatesh, Sanan / Vo, Maique / Vo, Nhat-Thi / Vo, Phuong / Voros, Timothy C / Wan, Yuan / Wang, Eric / Wang, Jeffrey / Wang, Michael K / Wang, Yuxuan / Wei, Siman / Wilson, Matthew N / Wong, Daniel / Wu, Elliott / Xing, Hanning / Xu, Jason P / Yaftaly, Sahar / Yan, Kimberly / Yang, Evan / Yang, Rebecca / Yao, Tony / Yeo, Patricia / Yip, Vivian / Yogi, Puja / Young, Gloria Chin / Yung, Maggie M / Zai, Alexander / Zhang, Christine / Zhang, Xiao X / Zhao, Zijun / Zhou, Raymond / Zhou, Ziqi / Abutouk, Mona / Aguirre, Brian / Ao, Chon / Baranoff, Alexis / Beniwal, Angad / Cai, Zijie / Chan, Ryan / Chien, Kenneth Chang / Chaudhary, Umar / Chin, Patrick / Chowdhury, Praptee / Dalie, Jamlah / Du, Eric Y / Estrada, Alec / Feng, Erwin / Ghaly, Monica / Graf, Rose / Hernandez, Eduardo / Herrera, Kevin / Ho, Vivien W / Honeychurch, Kaitlyn / Hou, Yurianna / Huang, Jo M / Ishii, Momoko / James, Nicholas / Jang, Gah-Eun / Jin, Daphne / Juarez, Jesse / Kesaf, Ayse Elif / Khalsa, Sat Kartar / Kim, Hannah / Kovsky, Jenna / Kuang, Chak Lon / Kumar, Shraddha / Lam, Gloria / Lee, Ceejay / Lee, Grace / Li, Li / Lin, Joshua / Liu, Josephine / Ly, Janice / Ma, Austin / Markovic, Hannah / Medina, Cristian / Mungcal, Jonelle / Naranbaatar, Bilguudei / Patel, Kayla / Petersen, Lauren / Phan, Amanda / Phung, Malcolm / Priasti, Nadiyah / Ruano, Nancy / Salim, Tanveer / Schnell, Kristen / Shah, Paras / Shen, Jinhua / Stutzman, Nathan / Sukhina, Alisa / Tian, Rayna / Vega-Loza, Andrea / Wang, Joyce / Wang, Jun / Watanabe, Rina / Wei, Brandon / Xie, Lillian / Ye, Jessica / Zhao, Jeffrey / Zimmerman, Jill / Bracken, Colton / Capili, Jason / Char, Andrew / Chen, Michel / Huang, Pingdi / Ji, Sena / Kim, Emily / Kim, Kenneth / Ko, Julie / Laput, Sean Louise G / Law, Sam / Lee, Sang Kuk / Lee, Olivia / Lim, David / Lin, Eric / Marik, Kyle / Mytych, Josh / O'Laughlin, Andie / Pak, Jensen / Park, Claire / Ryu, Ruth / Shinde, Ashwin / Sosa, Manny / Waite, Nick / Williams, Mane / Wong, Richard / Woo, Jocelyn / Woo, Jonathan / Yepuri, Vishaal / Yim, Dorothy / Huynh, Dan / Wijiewarnasurya, Dinali / Shapiro, Casey / Levis-Fitzgerald, Marc / Jaworski, Leslie / Lopatto, David / Clark, Ira E / Johnson, Tracy / Banerjee, Utpal

    G3 (Bethesda, Md.)

    2021  Volume 11, Issue 1

    Abstract: Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes ... ...

    Abstract Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.
    MeSH term(s) Animals ; Blood Cells ; Drosophila/genetics ; Genomics/education ; Humans ; Students ; Universities
    Language English
    Publishing date 2021-02-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkaa028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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