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author:("nyali, Shyam")
1.  Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes) 
Journal of phycology  2013;49(6):10.1111/jpy.12126.
We studied group I introns in sterile cultures of selected groups of lichen photobionts, focusing on Trebouxia species associated with Xanthoria s. lat. (including Xanthomendoza spp.; lichen-forming ascomycetes). Group I introns were found inserted after position 798 (Escherichia coli numbering) in the large subunit (LSU) rRNA in representatives of the green algal genera Trebouxia and Asterochloris. The 798 intron was found in about 25% of Xanthoria photobionts including several reference strains obtained from algal culture collections. An alignment of LSU-encoded rDNA intron sequences revealed high similarity of these sequences allowing their phylogenetic analysis. The 798 group I intron phylogeny was largely congruent with a phylogeny of the Internal Transcribed Spacer Region (ITS), indicating that the insertion of the intron most likely occurred in the common ancestor of the genera Trebouxia and Asterochloris. The intron was vertically inherited in some taxa, but lost in others. The high sequence similarity of this intron to one found in Chlorella angustoellipsoidea suggests that the 798 intron was either present in the common ancestor of Trebouxiophyceae, or that its present distribution results from more recent horizontal transfers, followed by vertical inheritance and loss. Analysis of another group I intron shared by these photobionts at small subunit (SSU) position 1512 supports the hypothesis of repeated lateral transfers of this intron among some taxa, but loss among others. Our data confirm that the history of group I introns is characterized by repeated horizontal transfers, and suggests that some of these introns have ancient origins within Chlorophyta.
PMCID: PMC3885279  PMID: 24415800
Lichen; LSU 798 group I intron; Photobiont; rbcL; SSU 1512 group I intron; Trebouxiophyceae; Trebouxia
2.  NanoLuc Reporter for Dual Luciferase Imaging in Living Animals 
Molecular imaging  2013;12(7):1-13.
Bioluminescence imaging is utilized widely for cell-based assays and animal imaging studies in biomedical research and drug development, capitalizing on high signal-to-background of this technique. A relatively small number of luciferases are available for imaging studies, substantially limiting the ability to image multiple molecular and cellular events as done commonly with fluorescence imaging. To advance dual reporter bioluminescence molecular imaging, we tested a recently developed, ATP-independent luciferase enzyme from Oplophorus gracilirostris (NanoLuc, NL) as a reporter for animal imaging. We demonstrated that NL could be imaged in superficial and deep tissues in living mice, although detection of NL in deep tissues was limited by emission of predominantly blue light by this enzyme. Changes in bioluminescence from NL over time could be used to quantify tumor growth, and secreted NL was detectable in small volumes of serum. We combined NL and firefly luciferase reporters to quantify two key steps in TGF-β signaling in intact cells and living mice, establishing a novel dual luciferase imaging strategy for quantifying signal transduction and drug targeting. Our results establish NL as new reporter for bioluminescence imaging studies in intact cells and living mice that will expand imaging of signal transduction in normal physiology, disease, and drug development.
PMCID: PMC4144862  PMID: 24371848
Bioluminescence; TGF-β; molecular imaging; luciferase; cell signaling
3.  Molecular Imaging of the ATM Kinase Activity 
Ataxia telangiectasia mutated (ATM) is a serine/threonine kinase critical to the cellular DNA-damage response, including from DNA double-strand breaks (DSBs). ATM activation results in the initiation of a complex cascade of events including DNA damage repair, cell cycle checkpoint control, and survival. We sought to create a bioluminescent reporter that dynamically and non-invasively measures ATM kinase activity in living cells and subjects.
Methods and Materials
Using the split luciferase technology we constructed a hybrid cDNA, ATM-reporter (ATMR), coding for a protein that quantitatively reports on changes in ATM kinase activity through changes in bioluminescence.
Treatment of ATMR expressing cells with ATM inhibitors resulted in a dose dependent increase in bioluminescence activity. In contrast, induction of ATM kinase activity upon irradiation resulted in a decrease in reporter activity that correlated with ATM and Chk2 activation by immunoblotting in a time-dependent fashion. Nuclear targeting improved ATMR sensitivity to both ATM inhibitors and radiation, while a mutant ATMR (lacking the target phosphorylation site) displayed a muted response. Treatment with ATM inhibitors and siRNA-targeted knockdown of ATM confirm the specificity of the reporter. Using reporter expressing xenografted tumors demonstrated the ability of ATMR to report in ATM activity in mouse models which correlated in a time-dependent fashion with changes in Chk2 activity.
We describe the development and validation of a novel, specific, non-invasive bioluminescent reporter that enables monitoring of ATM activity in real-time in vitro and in vivo. Potential applications of this reporter include the identification and development of novel ATM inhibitors or ATM-interacting partners through high-throughput screens, and in vivo pharmacokinetic/pharmacodynamic studies of ATM inhibitors in pre-clinical models.
PMCID: PMC3710537  PMID: 23726004
4.  Molecular Imaging of TGFβ-induced Smad2/3 phosphorylation reveals a role for receptor tyrosine kinases in modulating TGFβ signaling 
The dual modality of TGFβ, both as a potent tumor suppressor and a stimulator of tumor progression, invasion, and metastasis, make it a critical target for therapeutic intervention in human cancers. The ability to perform real-time, noninvasive imaging of TGFβ-activated Smad signaling in live cells and animal models would significantly improve our understanding of the regulation of this unique signaling cascade. To advance these efforts, we developed a highly sensitive molecular imaging tool that repetitively, non-invasively and dynamically reports on TGFBR1 kinase activity.
Experimental Design
The bioluminescent TGFβR1 reporter construct was developed using a split firefly luciferase gene containing a functional sensor of Smad2 phosphorylation wherein inhibition of TGFβ receptor1 kinase activity leads to an increase in reporter signaling. The reporter was stably transfected into mammalian cells and used to image in vivo and in vitro bioluminescent activity as a surrogate for monitoring TGFBR1 kinase activity.
The reporter was successfully used to monitor direct and indirect inhibitors of TGFβ-induced Smad2 and SMAD3 phosphorylation in live-cells and tumor xenografts and adapted for high throughput screening to identify a role for receptor tyrosine kinase-inhibitors as modulators of TGFβ signaling.
The reporter is a dynamic, non-invasive imaging modality for monitoring TGFβ-induced Smad2 signaling in live cells and tumor xenografts. It has immense potential for identifying novel effectors of R-Smad phosphorylation; for validating drug-target interaction; and for studying TGFβ signaling in different metastasis models.
PMCID: PMC3229686  PMID: 21948232
bioluminescence; kinase activity; non-invasive molecular imaging; receptor-regulated Smads; TGFβ
5.  A Novel Kinase Inhibitor of FADD Phosphorylation Chemosensitizes through the Inhibition of NF-κB 
Molecular cancer therapeutics  2011;10(10):1807-1817.
FADD (Fas-associated protein with death domain) is a cytosolic adapter protein essential for mediating death receptor-induced apoptosis. It has also been implicated in a number of non-apoptotic activities including embryogenesis, cell-cycle progression, cell proliferation, and tumorigenesis. Our recent studies have demonstrated that high levels of phosphorylated FADD in tumor cells correlates with increased activation of the anti-apoptotic transcription factor NF-κB and is a biomarker for aggressive disease and poor clinical outcome. These findings suggest that inhibition of FADD phosphorylation is a viable target for cancer therapy. A high throughput screen using a cell-based assay for monitoring FADD-kinase activity identified NSC 47147 as a small molecule inhibitor of FADD phosphorylation. The compound was evaluated in live cells and mouse tumors for its efficacy as an inhibitor of FADD-kinase activity through the inhibition of CK1α. NSC 47147 was shown to decrease levels of phosphorylated FADD and NF-κB activity such that combination therapy lead to greater induction of apoptosis and enhanced tumor control as compared to either agent alone. The studies described here demonstrate the utility of bioluminescent cell based assays for the identification of active compounds and the validation of drug target interaction in a living subject. In addition, the presented results provide proof of principle studies as to the validity of targeting FADD-kinase activity as a novel cancer therapy strategy.
PMCID: PMC3191281  PMID: 21859840
FADD; phosphorylation; non-invasive molecular imaging; NF-κB; chemotherapy
6.  Molecular Imaging of GSK3β and CK1α kinases 
Analytical biochemistry  2010;405(2):246-254.
Glycogen synthase kinase-3 (GSK3 β) and casein kinase-1 alpha (CK-1α) are multifunctional kinases that play critical role in the regulation of a number of cellular processes. In spite of their importance, molecular imaging tools for non-invasive and real-time monitoring of their kinase activities have not been devised. Here, we report development of bioluminescent GSK3β and CK-1α reporter (BGCR) based on firefly luciferase complementation. Treatment of SW620 cells stably expressing the reporter with inhibitors of GSK3β (SB415286 and LiCl) or CK1α (CKI-7) resulted in dose and time dependent increase in BGCR activity which were validated using western blotting. No increase in bioluminescence was observed in case of S37A mutant (GSK3β inhibitors) or with S45A mutant (CKI-7) demonstrating the specificity of the reporter. Imaging of mice tumor xenograft generated with BGCR expressing SW620 cells following treatment with LiCl showed unique oscillations in GSK3β activity which were corroborated by phospho-GSK3β immunoblotting. Taken together, BGCR is novel molecular imaging tool that reveals unique insight into GSK3β and CK1α kinase activities and may provide powerful tool in experimental therapeutics for rapid optimization of dose and schedule of targeted therapies and for monitoring therapeutic response.
PMCID: PMC2922438  PMID: 20561505
Molecular imaging; GSK3 β; CK1α; split luciferase; reporter
7.  High Throughput Molecular Imaging for the Identification of FADD Kinase Inhibitors 
Journal of biomolecular screening  2010;15(9):1063-1070.
Fas-Associated protein with Death Domain (FADD) was originally reported as a pro-apoptotic adaptor molecule that mediates receptor induced apoptosis. Recent studies have revealed a potential role of FADD in NF-κB activation, embryogenesis, and cell cycle regulation and proliferation. Over-expression of FADD and its phosphorylation have been associated with the transformed phenotype in many cancers and is therefore a potential target for therapeutic intervention. In an effort to delineate signaling events that lead to FADD phosphorylation and to identify novel compounds that impinge on this pathway, we developed a cell based reporter for FADD kinase activity. The reporter assay, optimized for a high throughput screen (HTS), measures bioluminescence in response to modulation of FADD kinase activity in live cells. In addition, the potential use of the reporter cell line in the rapid evaluation of pharmacologic properties of HTS hits in mouse models has been demonstrated.
PMCID: PMC3108567  PMID: 20855560
FADD; phosphorylation; non-invasive molecular imaging; bioluminescence; kinase activity
8.  Novel molecular imaging platform for monitoring oncological kinases 
Recent advances in oncology have lead to identification of a plethora of alterations in signaling pathways that are critical to oncogenesis and propagation of malignancy. Among the biomarkers identified, dysregulated kinases and associated changes in signaling cascade received the lion's share of scientific attention and have been under extensive investigations with goal of targeting them for anti-cancer therapy. Discovery of new drugs is immensely facilitated by molecular imaging technology which enables non-invasive, real time, dynamic imaging and quantification of kinase activity. Here, we review recent development of novel kinase reporters based on conformation dependent complementation of firefly luciferase to monitor kinase activity. Such reporter system provides unique insights into the pharmacokinetics and pharmacodynamics of drugs that modulate kinase signaling and have a huge potential in drug discovery, validation, and drug-target interactions.
PMCID: PMC2914645  PMID: 20615241

Results 1-8 (8)