Browsing by Author "Carey, Charles C."
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Item In situ gene expression profiling of the thermoacidophilic alga C yanidioschyzon in relation to visible and ultraviolet irradiance(2014-06) Skorupa, Dana J.; Castenholz, R. W.; Mazurie, Aurélien J.; Carey, Charles C.; Rosenzweig, F.; McDermott, Timothy R.Ultraviolet and high-intensity visible radiation generate reactive intermediates that damage phototrophic microorganisms. In Yellowstone National Park, the thermoacidophilic alga Cyanidioschyzon exhibits an annual seasonal biomass fluctuation referred to as 'mat decline', where algal viability decreases as ultraviolet and visible irradiances increase during summer. We examined the role irradiance might play in mat decline using irradiance filters that uncouple ultraviolet and visible effects along with custom microarrays to study gene expression in situ. Of the 6,507 genes, 88% showed no response to ultraviolet or visible, implying that at the biomolecular level, these algae inhabit a chemostat-like environment and is consistent with the near constant aqueous chemistry measured. The remaining genes exhibited expression changes linked to ultraviolet exposure, to increased visible radiation, or to the apparent combined effects of ultraviolet and visible. Expression of DNA repetitive elements was synchronized, being repressed by visible but also influenced by ultraviolet. At highest irradiance levels, these algae reduced transcription of genes encoding functions involved with DNA replication, photosynthesis and cell cycle progression but exhibited an uptick in activities related to repairing DNA damage. This corroborates known physiological responses to ultraviolet and visible radiation, and leads us to provisionally conclude that mat decline is linked to photoinhibition.Item Intensive herbicide use has selected for constitutively elevated levels of stress-responsive mRNAs and proteins in multiple herbicide-resistant Avena fatua L.(2017-08) Keith, Barbara K.; Burns, Erin E.; Bothner, Brian; Carey, Charles C.; Mazurie, Aurélien J.; Hilmer, Jonathan K.; Biyiklioglu, Sezgi; Budak, Hikmet; Dyer, William E.BACKGROUND: Intensive use of herbicides has led to the evolution two multiple herbicide-resistant (MHR) Avena fatua (wild oat) populations in Montana that are resistant to members of all selective herbicide families available for A. fatua control in U.S. small grain crops. We used transcriptome and proteome surveys to compare constitutive changes in MHR and herbicide susceptible (HS) plants associated with non-target site resistance (NTSR). RESULTS: Compared to HS plants, MHR plants contained constitutively elevated levels of differentially expressed genes (DEGs) with functions in xenobiotic catabolism, stress response, redox maintenance, and transcriptional regulation that are similar to abiotic-stress tolerant phenotypes. Proteome comparisons identified similarly elevated proteins including biosynthetic and multifunctional enzymes in MHR plants. Of 25 DEGs validated by RT-qPCR assay, differential regulation of 21 co-segregated with flucarbazone-sodium herbicide resistance in F3 families, and a subset of 10 of these were induced or repressed in herbicide-treated HS plants. CONCLUSIONS: Although the individual and collective contributions of these DEGs and proteins to MHR remain to be determined, our results support the idea that intensive herbicide use has selected for MHR populations with altered, constitutively-regulated patterns of gene expression that are similar to those in abiotic stress-tolerant plants. This article is protected by copyright. All rights reserved.Item A PAX5-OCT4-PRDM1 developmental switch specifies human primordial germ cells(2018-04) Fang, Fang; Angulo, Benjamin; Xia, Ninuo; Sukhwani, Meena; Wang, Zhengyuan; Carey, Charles C.; Mazurie, Aurélien J.; Cui, Jun; Wilkinson, Royce A.; Wiedenheft, Blake A.; Irie, Naoko; Surani, M. Azim; Orwig, Kyle E.; Reijo Pera, Renee A.Dysregulation of genetic pathways during human germ cell development leads to infertility. Here, we analysed bona fide human primordial germ cells (hPGCs) to probe the developmental genetics of human germ cell specification and differentiation. We examined the distribution of OCT4 occupancy in hPGCs relative to human embryonic stem cells (hESCs). We demonstrated that development, from pluripotent stem cells to germ cells, is driven by switching partners with OCT4 from SOX2 to PAX5 and PRDM1. Gain- and loss-of-function studies revealed that PAX5 encodes a critical regulator of hPGC development. Moreover, an epistasis analysis indicated that PAX5 acts upstream of OCT4 and PRDM1. The PAX5-OCT4-PRDM1 proteins form a core transcriptional network that activates germline and represses somatic programmes during human germ cell differentiation. These findings illustrate the power of combined genome editing, cell differentiation and engraftment for probing human developmental genetics that have historically been difficult to study.