scholarly journals Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware

2021 ◽  
Author(s):  
David Shallom ◽  
Danny Naiger ◽  
Shlomo Weiss ◽  
Tamir Tuller
Keyword(s):  
Mrna Translation ◽  
Whole Cell ◽  
Dedicated Hardware

Aquaporin-2 abundance in the renal collecting duct: new insights from cultured cell models

2009 ◽  
Vol 297 (1) ◽  
pp. F10-F18 ◽  
Author(s):  
Udo Hasler ◽  
Valérie Leroy ◽  
Pierre-Yves Martin ◽  
Eric Féraille
Keyword(s):  
Gene Transcription ◽  
Collecting Duct ◽  
Mrna Translation ◽  
Osmotic Gradient ◽  
Thick Ascending Limb ◽  
Whole Cell ◽  
Cell Abundance ◽  
Principal Cells ◽  
Aquaporin 2 ◽  
Aqp2 Gene

The renal cortico-papillary osmotic gradient is generated by sodium reabsorption in the thick ascending limb. The antidiuretic hormone arginine vasopressin (AVP) increases collecting duct water permeability by enhancing aquaporin-2 (AQP2) water channel insertion in the apical membrane of principal cells, allowing water to passively flow along the osmotic gradient from the tubule lumen to the interstitium. In addition to short-term AQP2 redistribution between intracellular compartments and the cell surface, AQP2 whole cell abundance is tightly regulated. AVP is a major transcriptional activator of the AQP2 gene, and stimulation of insulin- and calcium-sensing receptors respectively potentiate and reduce its action. Extracellular tonicity is another key factor that determines the levels of AQP2 abundance. Its effect is dependent on activation of the tonicity-responsive enhancer binding protein that reinforces AVP-induced AQP2 transcriptional activation. Conversely, activation of the NF-κB transcriptional factor by proinflammatory factors reduces AQP2 gene transcription. Aldosterone additionally regulates AQP2 whole cell abundance by simultaneously reducing AQP2 gene transcription and stimulating AQP2 mRNA translation. These examples illustrate how cross talk between various stimuli regulates AQP2 abundance in collecting duct principal cells and consequently contributes to maintenance of body water homeostasis.

HVEM Analysis of Microfilament Patterns in The Margins of Tissue Cells

1980 ◽  
Vol 38 ◽  
pp. 808-811
Author(s):  
Carol Allen
Keyword(s):  
Cell Movement ◽  
Cell Spreading ◽  
Living Cells ◽  
Tissue Cell ◽  
Large Sample Size ◽  
Cell Periphery ◽  
Whole Cell ◽  
Critical Point Drying ◽  
Lamellar Region ◽  
Tissue Cells

When provided with a suitable solid substrate, tissue cells undergo a rapid conversion from the spherical form expressed in suspension culture to a characteristic flattened morphology. As a result of this conversion, called cell spreading, the cell nucleus and organelles come to occupy a central region of “deep cytoplasm” which slopes steeply into a peripheral “lamellar” region less than 1 pm thick at its outer edge and generally free of cell organelles. Cell spreading is accomplished by a continuous outward repositioning of the lamellar margins. Cell translocation on the substrate results when the activity of the lamellae on one side of the cell become dominant. When this occurs, the cell is “polarized” and moves in the direction of the “leading lamellae”. Careful analysis of tissue cell locomotion by time-lapse microphotography (1) has shown that the deformational movements of the leading lamellae occur in a repeating cycle of advance and retreat in the direction of cell movement and that the rate of such deformations are positively correlated with the speed of cell movement. In the present study, the physical basis for these movements of the cell margin has been examined by comparative light microscopy of living cells with whole-mount electron microscopy of fixed cells. Ultrastructural observations were made on tissue cells grown on Formvar-coated grids, fixed with glutaraldehyde, further processed by critical-point drying, and then photographed in the High Voltage Electron Microscope. This processing and imaging system maintains the 3-dimensional organization of the whole cell, the relationship of the cell to the substrate, and affords a large sample size which facilitates quantitative analysis. Comparative analysis of film records of living cells with the whole-cell micrographs revealed that specific patterns of microfilament organization consistently accompany recognizable stages of lamellar formation and movement. The margins of spreading cells and the leading lamellae of locomoting cells showed a similar pattern of MF repositionings (Figs. 1-4). These results will be discussed in terms of a working model for the mechanics of lamellar motility which includes the following major features: (a) lamellar protrusion results when an intracellular force is exerted at a locally weak area of the cell periphery; (b) the association of cortical MFs with one another determines the local resistance to this force; (c) where MF-to-MF association is weak, the cell periphery expands and some cortical MFs are dragged passively forward; (d) contact of the expanded area with the substrate then triggers the lateral association and reorientation of these cortical MFs into MF bundles parallel to the direction of the expansion; and (e) an active interaction between these MF bundles associated with the cortex of the expanded lamellae and the cortical MFs which remained in the sub-lamellar region then pulls the latter MFs forward toward the expanded area. Thus, the advance of the cell periphery on the substrate occurs in two stages: a passive phase in which some cortical MFs are dragged outward by the force acting to expand the cell periphery, and an active phase in which additional cortical MFs are pulled forward by interaction with the first set. Subsequent interactions between peripheral microfilament bundles and filaments in the deeper cytoplasm could then transmit the advance gained by lamellar expansion to the bulk of the cytoplasm.

Permeability Through Bacterial Porins Dictates Whole Cell Compound Accumulation

2020 ◽  
Author(s):  
Silvia Acosta Gutiérrez ◽  
Igor Bodrenko ◽  
Matteo Ceccarelli
Keyword(s):  
Cell Envelope ◽  
Scoring Function ◽  
Modern Medicine ◽  
New Drugs ◽  
Prediction Ability ◽  
Whole Cell ◽  
Virtual Libraries ◽  
Major Bottleneck ◽  
Global Threat ◽  
Bacterial Porins

The lack of new drugs for Gram-negative pathogens is a global threat to modern medicine. The complexity of their cell envelope, with an additional outer membrane, hinders internal accumulation and thus, the access of molecules to targets. Our limited understanding of the molecular basis for compound influx and efflux from these pathogens is a major bottleneck for the discovery of effective antibacterial compounds. Here we analyse the correlation between the whole-cell compound accumulation of ~200 molecules and their predicted porin permeability coefficient (influx), using a recently developed scoring function. We found a strong linear relationship (75%) between the two, confirming porins key role in compound penetration. Further, the remarkable prediction ability of the scoring function demonstrates its potentiality to guide the optimization of hits to leads as well as the possibility of screening ultra-large virtual libraries. Eventually, the analysis of false positives, molecules with high-predicted influx but low accumulation, provides new hints on the molecular properties behind efflux.<br>

Lock-in Thermography-Based Local Efficiency Analysis of Solar Cells

2012 ◽  
Author(s):  
Otwin Breitenstein
Keyword(s):  
Solar Cells ◽  
Short Circuit ◽  
Efficiency Analysis ◽  
Open Circuit ◽  
Local Defect ◽  
Whole Cell ◽  
Local Efficiency ◽  
Cell Efficiency ◽  
Lock In ◽  
Efficiency Data

Abstract The electronic properties of solar cells, particularly multicrystalline silicon-based ones, are distributed spatially inhomogeneous, where regions of poor quality may degrade the performance of the whole cell. These inhomogeneities mostly affect the dark current-voltage (I-V) characteristic, which decisively affects the efficiency. Since the grid distributes the local voltage homogeneously across the cell and leads to lateral balancing currents, local light beam-induced current methods alone cannot be used to image local cell efficiency parameters. Lock-in thermography (LIT) is the method of choice for imaging inhomogeneities of the dark I-V characteristic. This contribution introduces a novel method for evaluating a number of LIT images taken at different applied biases. By pixel-wise fitting the data to a two diode model and taking into account local series resistance and short circuit current density data, realistically simulated images of the other cell efficiency parameters (open circuit voltage, fill factor, and efficiency) are obtained. Moreover, simulated local and global dark and illuminated I-V characteristics are obtained, also for various illumination intensities. These local efficiency data are expectation values, which would hold if a homogeneous solar cell had the properties of the selected region of the inhomogeneous cell. Alternatively, also local efficiency data holding for the cell working at its own maximum power point may be generated. The amount of degradation of different cell efficiency parameters in some local defect positions is an indication how dangerous these defects are for degrading this parameter of the whole cell. The method allows to virtually 'cut out' certain defects for checking their influence on the global characteristics. Thus, by applying this method, a detailed local efficiency analysis of locally inhomogeneous solar cells is possible. It can be reliably predicted how a cell would improve if certain defects could be avoided. This method is implemented in a software code, which is available.

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