Gene Expression Profiling Provides Insight into the Escape Behavior of Deepwater Rice During Submergence

2018 ◽  
Vol 61 (6) ◽  
pp. 374-382 ◽  
Author(s):  
Soong-Taek Hwang ◽  
Yeon-Ki Kim ◽  
Seong-Han Sohn ◽  
Dongsu Choi
2017 ◽  
Vol 439 ◽  
pp. 379-394 ◽  
Author(s):  
Sarah M. Romereim ◽  
Adam F. Summers ◽  
William E. Pohlmeier ◽  
Pan Zhang ◽  
Xiaoying Hou ◽  
...  

2014 ◽  
Vol 4 (1_suppl) ◽  
pp. s-0034-1376611-s-0034-1376611
Author(s):  
S. Grad ◽  
R. Gawri ◽  
L. Haglund ◽  
J. Ouellet ◽  
F. Mwale ◽  
...  

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. SCI-26-SCI-26
Author(s):  
Clark W. Distelhorst

Abstract SCI-26 Cell stress, if left unchecked, leads to apoptosis and autophagy. Both are highly conserved, genetically encoded processes. Apoptosis is a programmed death mechanism, designed to eliminate cells that are defective or no longer needed as part of developmental programs. Autophagy, on the other hand, is a programmed survival mechanism designed to provide cells a temporary source of energy when nutritionally deficient. Since in autophagy (“self eating”) the cell generates energy at the expense of its own organelles, temporary survival leads to death if nutrition is not restored. Both apoptosis and autophagy are induced by glucocorticosteroid hormone (GH) treatment of lymphoid malignancies. Since the main effects of GH on lymphocytes are metabolic, it is likely that apoptosis and autophagy are responses to metabolic stress. Metabolic stress occurs because GH inhibits both glucose uptake and metabolism, as well as calcium signals required for optimal mitochondrial function. Gene expression profiling has provided insight into the complex pathways that mediate apoptosis and autophagy in GH-treated leukemia and lymphoma cells. Ultimately, the balance of pro-apoptotic and anti-apoptotic factors determines cell fate. Elevation of the pro-apoptotic protein Bim is a critical step in apoptosis induction by GH and is due to GH-mediated repression of a microRNA cluster (miR17-95) that normally represses Bim expression. In metabolically stressed cells, Bim elevation is counterbalanced by a proton-sensing G protein-coupled receptor, TDAG8, that signals an elevation of the anti-apoptotic protein Bcl-2, counterbalancing Bim elevation and inhibiting apoptosis. Gene expression profiling also provided insight into the mechanism of autophagy by detecting GH-mediated repression of the Src kinases Fyn and Lck and GH-mediated elevation of Dig2 (REDD1, RTP801). Fyn and Lck interact with the inositol 1,4,5-trisphosphate calcium channel and promote physiological calcium signals. By decreasing Fyn and Lck, GH inhibits calcium signals necessary for optimal mitochondrial metabolism, contributing to autophagy induction. Dig2 is a stress protein that inhibits mTOR signaling. The absence of the Dig2 stress response in Dig2 knockout mice significantly impairs autophagy induction, decreasing lymphocyte survival in GH-treated mice. In summary, both apoptosis and autophagy occur in lymphoid malignancies in response to metabolic stress, as illustrated by the effects of GH treatment. A goal for future studies is to tie these signaling components together into a logical signaling network and to target components of the signaling network for therapeutic purposes. Disclosures: No relevant conflicts of interest to declare.


PLoS ONE ◽  
2018 ◽  
Vol 13 (12) ◽  
pp. e0208656 ◽  
Author(s):  
Shahid Hussain ◽  
Sonal Saxena ◽  
Sameer Shrivastava ◽  
Ashok Kumar Mohanty ◽  
Sudarshan Kumar ◽  
...  

2019 ◽  
Vol 57 (1) ◽  
pp. 30-38 ◽  
Author(s):  
Erin R Lewis ◽  
Sarah Geisbüsch ◽  
Yun-Juan Chang ◽  
Victor Costa ◽  
Seema Husain ◽  
...  

Abstract OBJECTIVES Thoracic endovascular techniques for aneurysm repair offer less invasive alternatives to open strategies. Both approaches, however, are associated with the risk for neurological complications. Despite adjuncts to maintain spinal cord perfusion, ischaemia and paraplegia continue to occur during thoracoabdominal aortic aneurysm (TAAA) repair. Staging of such extensive procedures has been proven to decrease the risk for spinal cord injury. Archived biopsy specimens may offer insight into the molecular signature of the reorganization and expansion of the spinal collateral network during staged endovascular interventions in the setting of TAAA. METHODS Biological replicates of total RNA were isolated from existing paraspinous muscle samples from 22 Yorkshire pigs randomized to 1 of 3 simulated TAAA repair strategies as part of a previous study employing coil embolization of spinal segmental arteries within the thoracic and lumbar spine. Gene expression profiling was performed using the Affymetrix GeneChip Porcine array. RESULTS Microarray analysis identified 649 differentially expressed porcine genes (≥1.3-fold change, P ≤ 0.05) when comparing paralysed and non-paralysed subjects. Of these, 355 were available for further analysis. When mapped to the human genome, 169 Homo sapiens orthologues were identified. Integrated interpretation of gene expression profiles indicated the significant regulation of transcriptional regulators (such as nuclear factor кB), cytokine (including CXCL12) elements contributing to hypoxia signalling in the cardiovascular system (vascular endothelial growth factor and UBE2) and cytoskeletal elements (like dystrophin (DMD) and matrix metallopeptidase (MMP)). CONCLUSIONS This study demonstrates the ability of microarray-based platforms to detect the differential expression of genes in paraspinous muscle during staged TAAA repair. Pathway enrichment analysis detected subcellular actors accompanying the neuroprotective effects of staged endovascular coiling. These observations provide new insight into the potential prognostic and therapeutic value of gene expression profiling in monitoring and modulating the arteriolar remodelling in the collateral network.


2003 ◽  
Vol 55 (6) ◽  
pp. 412-422 ◽  
Author(s):  
Kimmo Koskela ◽  
Pekka Kohonen ◽  
Pia Nieminen ◽  
Jean-Marie Buerstedde ◽  
Olli Lassila

2019 ◽  
Author(s):  
Jesse Q. Zhang ◽  
Christian A. Siltanen ◽  
Leqian Liu ◽  
Kai-Chun Chang ◽  
Zev J. Gartner ◽  
...  

AbstractSingle cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through gene expression alone. Linking sequencing with optical analysis has provided insight into the molecular basis behind cellular function, but current approaches have limited throughput. Here, we present a high throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements from thousands of cells in a single experiment and use the platform to characterize DNA and RNA changes in Jurkat cells through the cell cycle. In addition to its scalability, our integration of microfluidics and array-based molecular biology holds promise for comprehensive multi-omics profiling of single cells.


2011 ◽  
Vol 140 (5) ◽  
pp. S-13-S-14
Author(s):  
Michael E. Rothenberg ◽  
Tomer Kalisky ◽  
Piero D. Dalerba ◽  
Ysbrand Nusse ◽  
Stephen Quake ◽  
...  

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