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Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction [chapter]

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli
2009 Lecture Notes in Computer Science  
Conclusions: While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.  ...  The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction.  ...  A version of this paper was published in the WABI 2009 conference proceedings.  ... 
doi:10.1007/978-3-642-04241-6_12 fatcat:7e5q6vvkvbavlagt4b6qvf6ivq

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli
2010 Algorithms for Molecular Biology  
Conclusions: While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.  ...  The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction.  ...  A version of this paper was published in the WABI 2009 conference proceedings.  ... 
doi:10.1186/1748-7188-5-4 pmid:20047660 pmcid:PMC2826332 fatcat:yzqt7zn4afcwhnbgp22726nhbu

Behavioral Impairment in Aquatic Organisms Exposed to Neurotoxic Pollutants

Melissa Faria, Carlos Barata, Demetrio Raldúa
2022 Toxics  
Neuroactive chemicals are compounds that can modulate, at very low concentrations, the normal function of the central nervous systems of an organism through various primary modes of action (MoA) [...]  ...  The development of modern chemical screening approaches have allowed for the detection and quantification of many of these chemicals in parallel, confirming the co-occurrence in mixtures of many chemicals  ...  On the other hand, results that showed mixtures with both hyper-and hypoactivity-inducing components lead to an antagonistic interaction, and therefore, to qualitatively predict mixture outcomes of multi-complex  ... 
doi:10.3390/toxics10050243 fatcat:z5zf5wesmbgijmt5dgc4iainkm

Modulation of Gene Expression Regulated by the Transcription Factor NF-κB/RelA

Xueling Li, Yingxin Zhao, Bing Tian, Mohammad Jamaluddin, Abhishek Mitra, Jun Yang, Maga Rowicka, Allan R. Brasier, Andrzej Kudlicki
2014 Journal of Biological Chemistry  
Interacting proteins modulate the activity of NF-B/RelA transcription factor and expression of its targets.  ...  Significance: We provide new insight into the activity of NF-B/RelA. Our inference model can be applied to other processes and pathways.  ...  MIMOSA applies a mixture model and maximum expectation method to predict modulators of signal transducers and activators of transcription 1 (STAT1).  ... 
doi:10.1074/jbc.m113.539965 pmid:24523406 pmcid:PMC4002100 fatcat:w7gkxzxmingfljozwiwgavuudi

Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont

Delphine Capela, Marta Marchetti, Camille Clérissi, Anthony Perrier, Dorian Guetta, Carine Gris, Marc Valls, Alain Jauneau, Stéphane Cruveiller, Eduardo P.C. Rocha, Catherine Masson-Boivin
2017 Molecular biology and evolution  
Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146-3148, two of which encoding proteins likely associated to  ...  We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume  ...  Acknowledgements We are grateful to Lidwine Trouilh for helping in NimbleGen microarray hybridizations and Loic The complete collections of events generated for all the clones from this study are available  ... 
doi:10.1093/molbev/msx165 pmid:28535261 fatcat:qbpjglkh2zh3po4dtaj6wudyiy

Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

Philippe Remigi, Delphine Capela, Camille Clerissi, Léna Tasse, Rachel Torchet, Olivier Bouchez, Jacques Batut, Stéphane Cruveiller, Eduardo P. C. Rocha, Catherine Masson-Boivin, Jeffery L. Dangl
2014 PLoS Biology  
Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through  ...  serial plantbacteria co-cultures.  ...  Contributed to the writing of the manuscript: PR JB EPCR CMB.  ... 
doi:10.1371/journal.pbio.1001942 pmid:25181317 pmcid:PMC4151985 fatcat:m7ew2fnfcjdmvpv2lvwy7slnja

The Genetics of Plant Clocks [chapter]

C. Robertson McClung
2011 Advances in Genetics  
a copy to your institution's administrator.  ...  This chapter was originally published in the book Advances in Genetics, Vol. 74, published by Elsevier, and the attached copy is provided by Elsevier for the author's benefit and for the benefit of the  ...  The regulatory interactions among these loops are intricate and new ones continue to be revealed, adding to the complexity of our clock model.  ... 
doi:10.1016/b978-0-12-387690-4.00004-0 pmid:21924976 fatcat:y5zisftujzg5rmvlqjy6m4srs4

MicroRNA miR-1002 enhances NMNAT-mediated stress response by modulating alternative splicing

Joun Park, Yi Zhu, Xianzun Tao, Jennifer M. Brazill, Chong Li, Stefan Wuchty, R. Grace Zhai
2019 iScience  
Understanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies.  ...  These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.  ...  expression, we examined its binding sequence relative to known regulatory elements.  ... 
doi:10.1016/j.isci.2019.08.052 pmid:31522116 pmcid:PMC6745518 fatcat:hzpp2m64afavnjaetuofc6bu2e

Multidimensional analyses reveal modulation of adaptive and innate immune subsets by tuberculosis vaccines

Virginie Rozot, The C-040-404 Study Team, Elisa Nemes, Hennie Geldenhuys, Munyaradzi Musvosvi, Asma Toefy, Frances Rantangee, Lebohang Makhethe, Mzwandile Erasmus, Nicole Bilek, Simbarashe Mabwe, Greg Finak (+9 others)
2020 Communications Biology  
BCG revaccination increases frequencies of CD4 T cell subsets that either express Th1 cytokines or IL-22, and modestly increases IFNγ-producing NK cells.  ...  in discovery studies of correlates of protection.  ...  E.N. is a Marylou Ingram Scholar supported by the International Society for Advancement of Cytometry, and V.R. was supported by the Swiss National Foundation.  ... 
doi:10.1038/s42003-020-01288-3 pmid:33037320 fatcat:hq5tw5qucfd5fiaztpsmr3d4ue

Partner preference in the legume-rhizobia symbiosis and impact on legume inoculation strategies [chapter]

Stephane Boivin, Marc Lepetit
2019 Advances in Botanical Research  
The Quorum Sensing (QS) is a gene expression regulatory system acting at the level of bacterial populations (Papenfort & Bassler, 2016) .  ...  systems of Mimosa pudica have also been reported (Daubech et al., 2017) .  ... 
doi:10.1016/bs.abr.2019.09.016 fatcat:lkpi3nz2wvdk7ett32em357yr4

Nature-derived compounds modulating Wnt/β-catenin pathway: a preventive and therapeutic opportunity in neoplastic diseases

G. Sferrazza, M. Corti, G. Brusotti, P. Pierimarchi, C. Temporini, Annalucia Serafino, Enrica Calleri
2020 Acta Pharmaceutica Sinica B  
In this review we make an overview of the nature-derived compounds reported to have antitumor activity by modulating the Wnt/β-catenin signaling, also focusing on extraction methods, chemical features,  ...  The attention of the worldwide researchers paid to this issue is increasing, also in view of the therapeutic potential of these agents in diseases, such as Parkinson's disease (PD), for which no cure is  ...  Corti, and Annalucia Serafino co-worked to the writing of the manuscript and figures. P. Pierimarchi, C. Temporini critically reviewed the manuscript.  ... 
doi:10.1016/j.apsb.2019.12.019 pmid:33163337 pmcid:PMC7606110 fatcat:ppucbbbxmjct5ioyznkb7mf7ky

Control of a key transition from prostrate to erect growth in rice domestication

Lubin Tan, Xianran Li, Fengxia Liu, Xianyou Sun, Chenggang Li, Zuofeng Zhu, Yongcai Fu, Hongwei Cai, Xiangkun Wang, Daoxin Xie, Chuanqing Sun
2008 Nature Genetics  
Our results indicate that both AtSPX1 and AtSPX3 play positive roles in plant adaptation to phosphate starvation, and AtSPX3 may have a negative feedback regulatory role in AtSPX1 response to phosphate  ...  Activation of MPK3/MPK6 by expression of active upstream MAPK kinase (MAPKK) or MAPKK kinase (MAPKKK) was sufficient to induce camalexin synthesis in the absence of pathogen attack.  ...  Yang for critical reading of the manuscript.  ... 
doi:10.1038/ng.197 pmid:18820699 fatcat:m65q3yloy5gepoxcmx53kfk7yu

Keys to Symbiotic Harmony

W. J. Broughton, S. Jabbouri, X. Perret
2000 Journal of Bacteriology  
Flavonoids, the first of these, emanate from the plant and interact with rhizobial NodD proteins that serve as both environmental sensors and activators of transcription.  ...  Some flavonoids induce the expression of nodulation (nod, noe, and nol) and related genes (see reference 12), while others are catabolized (15, 79, 80) .  ...  Third, repressors such as NodD2 and NolR (29) further modulate nod gene expression.  ... 
doi:10.1128/jb.182.20.5641-5652.2000 pmid:11004160 pmcid:PMC94683 fatcat:33cltssuyzb3znup3dt4dxfkse

Abstracts of Presentations at IS-MPMI XVIII Congress

2019 Molecular Plant-Microbe Interactions  
Molecular Plant-Microbe Interactions 32:S1.1. https://doi.Contribution of a somatic hybridization event to the emergence of the Ug99 lineage of the wheat stem rust pathogen F.  ...  Contribution of a somatic hybridization event to the emergence of the Ug99 lineage of the wheat stem rust pathogen. (Abstr.)  ...  To address this, we used the yellow rust pathogen, Puccinia striiformis, as a model system to develop a computational approach that reduces the complexity of genomic data required for surveillance.  ... 
doi:10.1094/mpmi-32-10-s1.1 pmid:31573826 fatcat:othcerxdlrgwjiapockiozzfnq

Annexin5 Plays a Vital Role in Arabidopsis Pollen Development via Ca2+-Dependent Membrane Trafficking

Jingen Zhu, Xiaorong Wu, Shunjie Yuan, Dong Qian, Qiong Nan, Lizhe An, Yun Xiang, Girdhar K. Pandey
2014 PLoS ONE  
Overexpression of Ann5 did not affect pollen germination or pollen tube growth in response to LatB compared with wild-type, although Ann5 interacts with actin filaments in a manner similar to some animal  ...  These data demonstrated that Ann5 is involved in pollen development, germination and pollen tube growth through the promotion of endomembrane trafficking modulated by calcium.  ...  membrane and cytoskeleton interact and are modulated by Ca 2+ within pollen cells.  ... 
doi:10.1371/journal.pone.0102407 pmid:25019283 pmcid:PMC4097066 fatcat:mnkeh5gpbfdzbhiqegpfwkehma
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