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81.
We study the stochastic dynamics of growth and shrinkage of single actin filaments or microtubules taking into account insertion, removal, and ATP/GTP hydrolysis of subunits. The resulting phase diagram contains three different phases: two phases of unbounded growth: a rapidly growing phase and an intermediate phase, and one bounded growth phase. We analyze all these phases, with an emphasis on the bounded growth phase. We also discuss how hydrolysis affects force-velocity curves. The bounded growth phase shows features of dynamic instability, which we characterize in terms of the time needed for the ATP/GTP cap to disappear as well as the time needed for the filament to reach a length of zero (i.e., to collapse) for the first time. We obtain exact expressions for all these quantities, which we test using Monte Carlo simulations. 相似文献
82.
We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous work, we developed a model for a single actin or microtubule filament where hydrolysis occurred according to the vectorial mechanism: the filament could grow only from one end, and was in contact with a reservoir of monomers. Here we extend this approach in two ways—by including the dynamics of both ends and by comparing two possible mechanisms of ATP hydrolysis. Our emphasis is mainly on two possible limiting models for the mechanism of hydrolysis within a single filament, namely the vectorial or the random model. We propose a set of experiments to test the nature of the precise mechanism of hydrolysis within actin filaments. 相似文献
83.
Eleanor M. Townsend Leighann Sherry Ranjith Rajendran Donald Hansom John Butcher William G. Mackay 《Biofouling》2016,32(10):1259-1270
Chronic diabetic foot ulcers are frequently colonised and infected by polymicrobial biofilms that ultimately prevent healing. This study aimed to create a novel in vitro inter-kingdom wound biofilm model on complex hydrogel-based cellulose substrata to test commonly used topical wound treatments. Inter-kingdom triadic biofilms composed of Candida albicans, Pseudomonas aeruginosa, and Staphylococcus aureus were shown to be quantitatively greater in this model compared to a simple substratum when assessed by conventional culture, metabolic dye and live dead qPCR. These biofilms were both structurally complex and compositionally dynamic in response to topical therapy, so when treated with either chlorhexidine or povidone iodine, principal component analysis revealed that the 3-D cellulose model was minimally impacted compared to the simple substratum model. This study highlights the importance of biofilm substratum and inclusion of relevant polymicrobial and inter-kingdom components, as these impact penetration and efficacy of topical antiseptics. 相似文献
84.
Renate Auer D. Flemming Hansen Philipp Neudecker Dmitry M. Korzhnev D. Ranjith Muhandiram Robert Konrat Lewis E. Kay 《Journal of biomolecular NMR》2010,46(3):205-216
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR spectroscopy has emerged as a powerful tool for quantifying the
kinetics and thermodynamics of millisecond exchange processes between a major, populated ground state and one or more minor,
low populated and often invisible ‘excited’ conformers. Analysis of CPMG data-sets also provides the magnitudes of the chemical
shift difference(s) between exchanging states (|Δϖ|), that inform on the structural properties of the excited state(s). The
sign of Δϖ is, however, not available from CPMG data. Here we present one-dimensional NMR experiments for measuring the signs
of 1HN and 13Cα Δϖ values using weak off-resonance R
1ρ
relaxation measurements, extending the spin-lock approach beyond previous applications focusing on the signs of 15N and 1Hα shift differences. The accuracy of the method is established by using an exchanging system where the invisible, excited state
can be converted to the visible, ground state by altering conditions so that the signs of Δϖ values obtained from the spin-lock
approach can be validated with those measured directly. Further, the spin-lock experiments are compared with the established
H(S/M)QC approach for measuring the signs of chemical shift differences. For the Abp1p and Fyn SH3 domains considered here
it is found that while H(S/M)QC measurements provide signs for more residues than the spin-lock data, the two different methodologies
are complementary, so that combining both approaches frequently produces signs for more residues than when the H(S/M)QC method
is used alone. 相似文献
85.
86.
87.
Ranjith P. Anand Susan T. Lovett James E. Haber 《Cold Spring Harbor perspectives in biology》2013,5(12)
Recombination-dependent DNA replication, often called break-induced replication (BIR), was initially invoked to explain recombination events in bacteriophage but it has recently been recognized as a fundamentally important mechanism to repair double-strand chromosome breaks in eukaryotes. This mechanism appears to be critically important in the restarting of stalled and broken replication forks and in maintaining the integrity of eroded telomeres. Although BIR helps preserve genome integrity during replication, it also promotes genome instability by the production of loss of heterozygosity and the formation of nonreciprocal translocations, as well as in the generation of complex chromosomal rearrangements.The break-copy mode of recombination (as opposed to break-join), was initially proposed by Meselson and Weigle (1961). Break-copy recombination, now more commonly known as recombination-dependent DNA replication or break-induced replication (BIR), is believed to account for restarting replication at broken replication forks and may also play a central role in the maintenance of telomeres in the absence of telomerase. BIR has been studied in various model systems and has been invoked to explain chromosome rearrangements in humans. This review focuses primarily on mechanistic studies in Escherichia coli and its bacteriophages, T4 and λ, in the budding yeasts Saccharomyces cerevisiae and Kluyveromyces lactis and on apparently similar, but less well-documented, mechanisms in mammalian cells.Homology-dependent repair of DNA double-strand breaks (DSBs) occur by three major repair pathways (Pâques and Haber 1999) (Fig. 1). When both ends of the DNA share substantial homology with a donor template (a sister chromatid, a homologous chromosome, or an ectopically located segment), repair occurs almost exclusively by gene conversion (GC). If the DSB is flanked by direct repeats, then a second repair process, single-strand annealing (SSA), can occur as 5′ to 3′ resection of the DSB ends exposes complementary sequences that can anneal to each other and repair the break by the formation of a deletion. However, when only one DSB end shares homology with a donor sequence, repair occurs by BIR. There are two BIR pathways, one dependent on Rad51 recombinase and the other independent of Rad51.Open in a separate windowFigure 1.Three major repair pathways of homology-dependent recombination. Noncrossover (NCO) and crossover (CO) events are indicated. Black triangles represent resolution of Holliday junctions (HJs). Dashed lines represent new DNA synthesis. GC, gene conversion; SSA, single-strand annealing; BIR, break-induced replication. 相似文献
88.
Soumya S S Lakshmi Kavitha Sthanam Ranjith Padinhateeri Mandar M. Inamdar Shamik Sen 《PloS one》2014,9(9)
Physical properties of the extracellular matrix (ECM) are known to regulate cellular processes ranging from spreading to differentiation, with alterations in cell phenotype closely associated with changes in physical properties of cells themselves. When plated on substrates of varying stiffness, fibroblasts have been shown to exhibit stiffness matching property, wherein cell cortical stiffness increases in proportion to substrate stiffness up to 5 kPa, and subsequently saturates. Similar mechanoadaptation responses have also been observed in other cell types. Trypsin de-adhesion represents a simple experimental framework for probing the contractile mechanics of adherent cells, with de-adhesion timescales shown to scale inversely with cortical stiffness values. In this study, we combine experiments and computation in deciphering the influence of substrate properties in regulating de-adhesion dynamics of adherent cells. We first show that NIH 3T3 fibroblasts cultured on collagen-coated polyacrylamide hydrogels de-adhere faster on stiffer substrates. Using a simple computational model, we qualitatively show how substrate stiffness and cell-substrate bond breakage rate collectively influence de-adhesion timescales, and also obtain analytical expressions of de-adhesion timescales in certain regimes of the parameter space. Finally, by comparing stiffness-dependent experimental and computational de-adhesion responses, we show that faster de-adhesion on stiffer substrates arises due to force-dependent breakage of cell-matrix adhesions. In addition to illustrating the utility of employing trypsin de-adhesion as a biophysical tool for probing mechanoadaptation, our computational results highlight the collective interplay of substrate properties and bond breakage rate in setting de-adhesion timescales. 相似文献
89.
The study was aimed at investigating localized topical drug delivery to the breast via mammary papilla (nipple). 5-fluorouracil (5-FU) and estradiol (EST) were used as model hydrophilic and hydrophobic compounds respectively. Porcine and human nipple were used for in-vitro penetration studies. The removal of keratin plug enhanced the drug transport through the nipple. The drug penetration was significantly higher through the nipple compared to breast skin. The drug’s lipophilicity had a significant influence on drug penetration through nipple. The ducts in the nipple served as a major transport pathway to the underlying breast tissue. Results showed that porcine nipple could be a potential model for human nipple. The topical application of 5-FU on the rat nipple resulted in high drug concentration in the breast and minimal drug levels in plasma and other organs. Overall, the findings from this study demonstrate the feasibility of localized drug delivery to the breast through nipple. 相似文献
90.
Jue Lu Rankothge Ranjith Weerasiri Yan Liu Wei Wang Shaowen Ji Ilsoon Lee 《Biotechnology and bioengineering》2013,110(8):2123-2130
Cellulase, xylanase, and β‐glucosidase production was studied on novel nano‐shear pretreated corn stover by the mixed fungi culture. The high shear force from a modified Tayor‐Couette nano‐shear mixing reactor efficiently disintegrated corn stover, resulting in a homogeneous watery mash with particles in much reduced size. Scanning electron microscope study showed visible mini‐pores on the fiber cell wall surface, which could improve the accessibility of the pretreated corn stover to microorganisms. Mixed fungal culture of Trichoderma reesei RUT‐C30 and Aspergillus niger produced enzymes with higher cellulolytic and xylanolytic activities on corn stover pretreated with nano‐shear mixing reactor, in comparison with other pretreatment methods, including acid and ammonia fiber explosion (AFEX) pretreatment. The hydrolytic potential of the whole fermentation broth from the mixed fungi was studied, and the possibility of applying the whole cell saccharification concept was also investigated to further reduce the cost of lignocellulose hydrolysis. Biotechnol. Bioeng. 2013; 110: 2123–2130. © 2013 Wiley Periodicals, Inc. 相似文献