scholarly journals The depletion attraction: an underappreciated force driving cellular organization

2006 ◽  
Vol 175 (5) ◽  
pp. 681-686 ◽  
Author(s):  
Davide Marenduzzo ◽  
Kieran Finan ◽  
Peter R. Cook
Keyword(s):  
Van Der Waals ◽  
Cellular Structures ◽  
Cellular Organization ◽  
Chromatin Loops ◽  
Wide Range ◽  
Ionic Bonds ◽  
In Cells

Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force—the “depletion attraction”—also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.

Efficient Prediction of Structural and Electronic Properties of Hybrid 2D Materials Using DFT and Machine Learning

2018 ◽  
Author(s):  
Sherif Tawfik ◽  
Olexandr Isayev ◽  
Catherine Stampfl ◽  
Joseph Shapter ◽  
David Winkler ◽  
...  
Keyword(s):  
Machine Learning ◽  
Band Gap ◽  
Density Functional ◽  
2D Materials ◽  
Van Der Waals ◽  
Building Blocks ◽  
Machine Learning Techniques ◽  
Interlayer Distance ◽  
Computational Screening ◽  
Wide Range

Materials constructed from different van der Waals two-dimensional (2D) heterostructures offer a wide range of benefits, but these systems have been little studied because of their experimental and computational complextiy, and because of the very large number of possible combinations of 2D building blocks. The simulation of the interface between two different 2D materials is computationally challenging due to the lattice mismatch problem, which sometimes necessitates the creation of very large simulation cells for performing density-functional theory (DFT) calculations. Here we use a combination of DFT, linear regression and machine learning techniques in order to rapidly determine the interlayer distance between two different 2D heterostructures that are stacked in a bilayer heterostructure, as well as the band gap of the bilayer. Our work provides an excellent proof of concept by quickly and accurately predicting a structural property (the interlayer distance) and an electronic property (the band gap) for a large number of hybrid 2D materials. This work paves the way for rapid computational screening of the vast parameter space of van der Waals heterostructures to identify new hybrid materials with useful and interesting properties.

Two-Color Probe to Monitor a Wide Range of pH Values in Cells

2013 ◽  
Vol 52 (24) ◽  
pp. 6206-6209 ◽  
Author(s):  
Min Hee Lee ◽  
Ji Hye Han ◽  
Jae Hong Lee ◽  
Nayoung Park ◽  
Rajesh Kumar ◽  
...  
Keyword(s):  
Ph Values ◽  
Wide Range ◽  
In Cells

A novel electrochemical conducting polymer sensor for the rapid, selective and sensitive detection of biothiols

2021 ◽  
Author(s):  
Bicheng Zhu ◽  
Devon Bryant ◽  
Alireza Akbarinejad ◽  
Jadranka Travas-Sejdic ◽  
Lisa I Pilkington
Keyword(s):  
Conducting Polymer ◽  
Sensitive Detection ◽  
Bodily Fluids ◽  
Wide Range ◽  
In Cells

Biological thiols (biothiols) in cells and bodily fluids are intrinsically linked to the functioning of important enzymes, deficiency in which can lead to a wide range of physiological and pathological...

Two-Color Probe to Monitor a Wide Range of pH Values in Cells

2013 ◽  
Vol 125 (24) ◽  
pp. 6326-6329 ◽  
Author(s):  
Min Hee Lee ◽  
Ji Hye Han ◽  
Jae Hong Lee ◽  
Nayoung Park ◽  
Rajesh Kumar ◽  
...  
Keyword(s):  
Ph Values ◽  
Wide Range ◽  
In Cells

scholarly journals A validated collection of mouse monoclonal antibodies to human glycosyltransferases functioning in mucin-type O-glycosylation

Glycobiology ◽  
2019 ◽  
Vol 29 (9) ◽  
pp. 645-656 ◽  
Author(s):  
Catharina Steentoft ◽  
Zhang Yang ◽  
Shengjun Wang ◽  
Tongzhong Ju ◽  
Malene B Vester-Christensen ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Secretory Pathway ◽  
Expression Patterns ◽  
In Situ Monitoring ◽  
Kinetic Properties ◽  
Detailed Knowledge ◽  
Cellular Expression ◽  
Wide Range ◽  
Catalytically Active ◽  
In Cells

Abstract Complex carbohydrates serve a wide range of biological functions in cells and tissues, and their biosynthesis involves more than 200 distinct glycosyltransferases (GTfs) in human cells. The kinetic properties, cellular expression patterns and subcellular topology of the GTfs direct the glycosylation capacity of a cell. Most GTfs are ER or Golgi resident enzymes, and their specific subcellular localization is believed to be distributed in the secretory pathway according to their sequential role in the glycosylation process, although detailed knowledge for individual enzymes is still highly fragmented. Progress in quantitative transcriptome and proteome analyses has greatly advanced our understanding of the cellular expression of this class of enzymes, but availability of appropriate antibodies for in situ monitoring of expression and subcellular topology have generally been limited. We have previously used catalytically active GTfs produced as recombinant truncated secreted proteins in insect cells for generation of mouse monoclonal antibodies (mAbs) to human enzymes primarily involved in mucin-type O-glycosylation. These mAbs can be used to probe subcellular topology of active GTfs in cells and tissues as well as their presence in body fluids. Here, we present several new mAbs to human GTfs and provide a summary of our entire collection of mAbs, available to the community. Moreover, we present validation of specificity for many of our mAbs using human cell lines with CRISPR/Cas9 or zinc finger nuclease (ZFN) knockout and knockin of relevant GTfs.

scholarly journals Spinophilin and the immune synapse

2008 ◽  
Vol 181 (2) ◽  
pp. 181-183 ◽  
Author(s):  
Brian Seed ◽  
Ramnik Xavier
Keyword(s):  
T Cells ◽  
Dendritic Cells ◽  
Fusion Protein ◽  
Target Cells ◽  
Cellular Organization ◽  
Immune Synapse ◽  
Cellular Architecture ◽  
Gfp Fusion Protein ◽  
Cell Biol ◽  
In Cells

Extensive alterations in cellular organization are known to accompany the responses of sensitized T cells to target cells presenting an antigen of interest. Now, equally if not more dramatic changes are found to take place in cells presenting an antigen. With the help of a spinophilin-GFP fusion protein, Bloom et al. (Bloom, O., J.J. Unternaehrer, A. Jiang, J.-S. Shin, L. Delamarre, P. Allen, and I. Mellman. 2008. J. Cell Biol. 181:203–211) have captured a remarkable polarization of the cellular architecture of dendritic cells presenting an antigen to T cells.

STAT3 Activates Anti-Apoptotic Genes But When In Access Induces Apoptosis Of CLL Cells

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 5294-5294 ◽  
Author(s):  
Rozovski Uri ◽  
David Harris ◽  
Ping Li ◽  
Zhiming Liu ◽  
Ji Yuan ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Caspase 3 ◽  
Conflicts Of Interest ◽  
Lymphocytic Leukemia ◽  
Luciferase Assay ◽  
Spontaneous Apoptosis ◽  
Mobility Shift ◽  
Apoptotic Pathway ◽  
Wide Range ◽  
In Cells

Abstract In chronic lymphocytic leukemia (CLL) cells, signal transducer and activator of transcription 3 (STAT3) is constitutively phosphorylated on serine 727 residues, and phosphoserine STAT3 induces the transcription and proliferation of anti-apoptosis genes including c-Myc, BCL2, Bcl-XL, and Mcl-1 (Hazan-Halevy, 2010). Therefore, we hypothesized that the CLL cells of patients with high peripheral blood absolute lymphocyte counts (ALCs) have a high level of STAT3 protein expression and a low rate of spontaneous apoptosis. Using Western blotting and flow cytometry, we quantitated STAT3 levels and apoptosis rates in CLL cells from 64 patients with high (N=32) and low (N=32) ALCs. As expected, the levels of STAT3 expression were significantly higher in cells from patients with high ALCs (145,000 ± 49,738/µL) than in cells from patients with low ALCs (12,800 ± 4,654/µL). However, contrary to our hypothesis, Annexin V/PI staining revealed that the levels of procaspase-3, its activated (cleaved) form caspase-3, and cleaved PARP as well as the apoptosis rates of cells from patients with high ALCs were significantly higher than those in cells from patients with low ALCs. These findings suggest that cells from patients with high ALCs are prone to spontaneous apoptosis. An RNA microarray analysis revealed that the levels of apoptotic pathway genes were upregulated in cells from patients with high ALC (P = 0.002), and Reverse-transcriptaction PCR of Caspase-3, Calpain 9, MAPK 8, KRAS, PLCγ-2, and PKC validated the array data. Intrigued by these findings, we sought to determine whether high levels of intracellular STAT3 induce apoptosis. Indeed, overexpression of STAT3 in interleukin-6–stimulated MM1 cells upregulated caspase-3 and caspase-3 protein levels and induced apoptosis. Similarly, in CLL cells levels of caspase3 and procaspase3 remained stable across a wide range of STAT3 levels, but when STAT3 reached a threshold, level of caspase3 and procaspase3 markedly increased. Because sequence analysis revealed that the caspase-3 promoter harbors γ-interferon activation sequence-like elements, we cloned the caspase-3 promoter in MM1 cells and, using a luciferase assay, identified regions with putative STAT3 binding sites. Chromatin immunoprecipitation (ChIP) and an electrophoretic mobility shift essay (EMSA) confirmed that STAT3 binds to the promoter of caspase-3. However, caspase-3 was activated only in cells with high STAT3 expression levels, suggesting that STAT3 binds to caspase-3 with low affinity. To assess STAT3’s binding affinity to the caspase-3 promoter, we prepared serial dilutions of CLL cell DNA and, using ChIP and EMSA, found that STAT3’s binding affinities to p21 and c-Myc were 8 and 4 times as high, respectively, as its binding affinity to caspase-3, suggesting that high levels of STAT3 protein are required to activate caspase-3. Taken together, these findings suggest that activated STAT3 has a previously unknown pro-apoptotic function. At high intracellular levels, rather than providing CLL cells with survival advantage, STAT3 induces apoptosis by activating caspase-3. Thus, because CLL cell proliferation is coupled with spontaneous CLL cell apoptosis, the number of circulating CLL cells based on the cells’ proliferation rate is often lower than expected. Disclosures: No relevant conflicts of interest to declare.

TOWARDS A MOLECULAR THEORY FOR THE VAN DER WAALS–MAXWELL DESCRIPTION OF FLUID PHASE TRANSITIONS

2002 ◽  
Vol 01 (02) ◽  
pp. 381-406 ◽  
Author(s):  
ANDRIY KOVALENKO ◽  
FUMIO HIRATA
Keyword(s):  
Hydrogen Bonding ◽  
Phase Transitions ◽  
Phase Diagrams ◽  
Equations Of State ◽  
Van Der Waals ◽  
Fluid Phase ◽  
Carbon Aerogel ◽  
Molecular Fluids ◽  
Wide Range ◽  
Realistic Interaction

We briefly review developments of theories for phase transitions of molecular fluids and mixtures, from semi-phenomenological approaches providing equations of state with adjustable parameters to first-principles microscopic methods qualitatively correct for a variety of molecular models with realistic interaction potentials. We further present the generalization of the van der Waals–Maxwell description of fluid phase diagrams to account for chemical specificities of polar molecular fluids, such as hydrogen bonding. Our theory uses the reference interaction site model (RISM) integral equation approach complemented with the new closure we have proposed (KH approximation), successful over a wide range of density from gas to liquid. The RISM/KH theory is applied to the known three-site models of water, methanol, and hydrogen fluoride. It qualitatively reproduces their vapor-liquid phase diagrams and the structure in the gas as well as liquid phases, including hydrogen bonding. Furthermore, phase transitions of water and methanol sorbed in nanoporous carbon aerogel are described by means of the replica generalization of the RISM approach we have developed. The changes as compared to the bulk fluids are in agreement with simulations and experiment. The RISM/KH theory is promising for description of phase transitions in various associating fluids, in particular, electrolyte as well as non-electrolyte solutions and ionic liquids.

scholarly journals Enhancement of homology-directed repair with chromatin donor templates in cells

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Grisel Cruz-Becerra ◽  
James T Kadonaga
Keyword(s):  
Genome Editing ◽  
Dna Fragments ◽  
Natural Form ◽  
Naked Dna ◽  
Homology Directed Repair ◽  
Coding Regions ◽  
Wide Range ◽  
Low Efficiency ◽  
Donor Template ◽  
In Cells

A key challenge in precise genome editing is the low efficiency of homology-directed repair (HDR). Here we describe a strategy for increasing the efficiency of HDR in cells by using a chromatin donor template instead of a naked DNA donor template. The use of chromatin, which is the natural form of DNA in the nucleus, increases the frequency of HDR-edited clones as well as homozygous editing. In addition, transfection of chromatin results in negligible cytotoxicity. These findings suggest that a chromatin donor template should be useful for a wide range of HDR applications such as the precise insertion or replacement of DNA fragments that contain the coding regions of genes.

scholarly journals Manipulable Electronic and Optical Properties of Two-Dimensional MoSTe/MoGe2N4 van der Waals Heterostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3338
Author(s):  
Jiali Wang ◽  
Xiuwen Zhao ◽  
Guichao Hu ◽  
Junfeng Ren ◽  
Xiaobo Yuan
Keyword(s):  
Optical Properties ◽  
Absorption Coefficient ◽  
High Performance ◽  
Density Functional ◽  
Van Der Waals ◽  
Two Dimensional ◽  
Van Der Waals Heterostructures ◽  
Electronic And Optical Properties ◽  
Wide Range ◽  
Direct Band

van der Waals heterostructures (vdWHs) can exhibit novel physical properties and a wide range of applications compared with monolayer two-dimensional (2D) materials. In this work, we investigate the electronic and optical properties of MoSTe/MoGe2N4 vdWH under two different configurations using the VASP software package based on density functional theory. The results show that Te4-MoSTe/MoGe2N4 vdWH is a semimetal, while S4-MoSTe/MoGe2N4 vdWH is a direct band gap semiconductor. Compared with the two monolayers, the absorption coefficient of MoSTe/MoGe2N4 vdWH increases significantly. In addition, the electronic structure and the absorption coefficient can be manipulated by applying biaxial strains and changing interlayer distances. These studies show that MoSTe/MoGe2N4 vdWH is an excellent candidate for high-performance optoelectronic devices.

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