Theoretical Study of Pulled Polymer Loops as a Model for Fission Yeast Chromosome

In this thesis, we study the physics of the pulled polymer loops motivated by a biological problem of chromosome alignment during meiosis in fission yeast. During prophase I of meiotic fission yeast, the chromosomes form a loop structure by binding their telomeres to the Spindle Pole Body (SPB). SPB nucleates the growth of microtubules in the cytoplasm. Molecular motors attached to the cell membrane can exert the force on the microtubules and thus pull the whole nucleus. The nucleus performs oscillatory motion from one to the other end of the elongated zygote cell. Experimental evidence suggests that these oscillations facilitate homologous chromosome alignment which is required for the gene recombination. Our goal is to understand the physical mechanism of this alignment. We thus propose a model of pulled polymer loops to represent the chromosomal motion during oscillations. Using a freely-jointed bead-rod model for the pulled polymer loop, we solve the equilibrium statistics of the polymer configurations both in 1D and 3D. In 1D, we find a peculiar mapping of the bead-rod system to a system of particles on a lattice. Utilizing the wealth of tools of the particle system, we solve exactly the 1D stationary measure and map it back to the polymer system. To address the looping geometry, the Brownian Bridge technique is employed. The mean and variance of beads position along the loop are discussed in detail both in 1D and 3D. We then can calculate the three-dimensional statistics of the distance between corresponding beads from a pair of loops in order to discuss the pairing problem of homologous chromosomes. The steady-state shape of a three-dimensional pulled polymer loop is quantified using the descriptors based on the gyration tensor. Beyond the steady state statistics, the relaxation dynamics of the pinned polymer loop in a constant external force field is discussed. In 1D we show the mapping of polymer dynamics to the well-known Asymmetric Simple Exclusion Process (ASEP) model. Our pinned polymer loop is mapped to a half-filled ASEP with reflecting boundaries. We solve the ASEP model exactly by using the generalized Bethe ansatz method. Thus with the help of the ASEP theory, the relaxation time of the polymer problem can be calculated analytically. To test our theoretical predictions, extensive simulations are performed. We find that our theory of relaxation time fit very well to the relaxation time of a 3D polymer in the direction of the external force field. Finally, we discuss the relevance of our findings to the problem of chromosome alignment in fission yeast

Effects of EGR rates on combustion and emission characteristics in a diesel engine with n-butanol/PODE3-4/diesel blends

An experimental investigation is conducted on the influence of EGR (Exhaust Gas Recirculation) rates (0–40%) on the combustion and emission characteristics of n-butanol/diesel/PODE3-4 blends at low-temperature combustion mode in diesel engine. The results show that at identical EGR rate, compared to D100 (diesel fuel), the peak values both of the mean cylinder pressure and the heat release rate of BD20 (20% butanol and 80% diesel in volume) are increased, ignition delay is extended, and the brake thermal efficiency is enhanced. Concerning BD20 blended with PODE3-4, the ignition delay is shortened, while both the brake thermal efficiency and the combustion efficiency increase. At the EGR rate below 30%, as the EGR rate grows, the effects on emission of soot, CO and HC are not significant, while the emission of NOx is sharply reduced; when the EGR rate is above 30%, as it grows, the emissions of soot, CO, and HC drastically rise. As EGR rate grows, the total particulate matter (PM) number concentrations of four fuels firstly decline and then rise, the total PM mass concentrations keep stable firstly and then rise drastically. As the proportion of added PODE3-4 in BD20 grows, the particle geometric mean diameters further decrease

Process optimization in the extract of perilla seed oil with plant protein hydrolysate complex enzyme

Abstract Perilla seed oil riched in the ω-3 fatty acid especially α-linolenic acid, is associated with a beneficial role in human health. In the present study, Aqueous Enzymatic Extraction (AEE) of crude oil from Perilla seeds was investigated. The extraction parameters of Perilla seed oil including enzyme type, solid-to-water ratio, pH, temperature, enzyme loading and hydrolysis time were determined by Response Surface Methodology (RSM). The RSM results showed the optimum extraction enzyme for Perilla oil was plant protein hydrolysate complex enzyme. The optimized values of solid-to-water ratio, pH, temperature, enzyme loading, and hydrolysis time for extracting oil from perilla seeds respectively were 1:4, 6, 55 °C, 2% and 4.5 h. Under the conditions, the maximum oil recovery of perilla oil was 88.52%, perilla seed oil extracted by AEE possessed a high extraction yield

Unraveling the molecular mechanisms of thermo-responsive properties of silk-elastin-like proteins by integrating multiscale modeling and experiment

Adaptive hydrogels tailor-made from silk-elastin-like proteins (SELPs) possess excellent biocompatibility and biodegradability with properties that are tunable and responsive to multiple simultaneous external stimuli. To unravel the molecular mechanisms of their physical response to external stimuli in tandem with experiments, here we predict and measure the variation in structural properties as a function of temperature through coarse-grained (CG) modeling of individual and crosslinked SE8Y and S4E8Y molecules, which have ratios of 1:8 and 4:8 of silk to elastin blocks respectively. Extensive structural reshuffling in single SE8Y molecules led to the increased compactness of the structure, whereas S4E8Y molecules did not experience any significant changes as they already adopted very compact structures at low temperatures. Crosslinking of SE8Y molecules at high concentrations impeded their structural transition at high temperatures that drastically reduced the degree of deswelling through extensive suppression of the structural shuffling and the trapping of the molecules in high potential energy states due to inter-molecular constraints. This integrative experimental and computational understanding of the thermal response in single molecules of SELPs and their crosslinked networks should lead to further improvements in the properties of SELP hydrogels through predictive designs and their wider applications in biomaterials and tissue engineering.United States. Department of Defense. Office of Naval Research (Grant N00014-16-1-233)United States. National Institutes of Health (Grant U01 EB014976)Singapore. Agency for Science, Technology and Research (Grant A1786a0031)United States. National Science Foundation. (Grant ACI-1053575

Microbial Properties Depending on Fertilization Regime in Agricultural Soils with Different Texture and Climate Conditions: A Meta-Analysis

Over-fertilization has a significant impact on soil microbial properties and its ecological environment. However, the effects of long-term fertilization on microbial properties on a large scale are still vague. This meta-analysis collected 6211 data points from 109 long-term experimental sites in China to evaluate the effects of fertilizer type and fertilization duration, as well as soil and climate conditions, on the effect sizes on various microbial properties and indices. The organic fertilizers combined with straw (NPKS) and manure (NPKM) had the highest effect sizes, while the chemical fertilizers N (sole N fertilizer) and NPK (NPK fertilizer) had the lowest. When compared with the control, NPKM treatment had the highest effect size, while N treatment had the lowest effect size on MBN (111% vs. 19%), PLFA (110% vs. −7%), fungi (88% vs. 43%), Actinomycetes (97% vs. 44%), urease (77% vs. 25%), catalase (15% vs. −11%), and phosphatase (58% vs. 4%). NPKM treatment had the highest while NPK treatment had the lowest effect size on bacteria (123% vs. 33%). NPKS treatment had the highest while N treatment had the lowest effect sizes on MBC (77% vs. 8%) and invertase (59% vs. 0.2%). NPKS treatment had the highest while NPK treatment had the lowest effect size on the Shannon index (5% vs. 1%). The effect sizes of NPKM treatment were the highest predominantly in arid regions because of the naturally low organic carbon in soils of these regions. The effect sizes on various microbial properties were also highly dependent on soil texture. In coarse-textured soils the effect sizes on MBC and MBN peaked sooner compared with those of clayey or silty soils, although various enzymes were most active in silty soils during the first 10 years of fertilization. Effect sizes on microbial properties were generally higher under NPKM and NPKS treatments than under NPK or N treatments, with considerable effects due to climate conditions. The optimal field fertilizer regime could be determined based on the effects of fertilizer type on soil microorganisms under various climate conditions and soil textures. This will contribute to the microbial biodiversity and soil health of agricultural land. Such controls should be used for adaptation of fertilization strategies to global changes

Biosynthesis, characterization, and antifungal activity of plant-mediated silver nanoparticles using Cnidium monnieri fruit extract

The present study describes a novel method for green synthesis of silver nanoparticles using Cnidium monnieri (CM-AgNPs). Cnidium monnieri fruit is an excellent anti tinea drug that can be used externally to treat superficial fungal infections in the human body. The aqueous ethanolic extract of Cnidium monnieri fruit was prepared and employed in the synthesis of stable silver nanoparticles via biological reduction method. The synthesis conditions of CM-AgNPs was systematically optimized using Box–Behnken design. CM-AgNPs were well characterized by UV-spectroscopy and X-ray powder diffraction (XRD), and it was confirmed that the synthesized particles were AgNPs. The possible functional groups required for the reduction and stabilization of CM-AgNPs in the extract were identified through FTIR spectrum. The size of CM-AgNPs structure was confirmed to be approximately 44.6 nm in polydisperse spherical shape through scanning electron microscopy (SEM), transmission electron microscopy (TEM), and laser dynamic light scattering (DLS). Further, the minimum inhibitory concentration 90% (MIC90) ratios values of Cm-AgNPs against Trichophyton rubrum (7 d), T. mentagrophytes (7 d) and Candida albicans (24 h) were 3.125, 3.125, and 0.78125 μg/mL, respectively, determined by the broth micro dilution method. Finally, the result was concluded that the synthesized AgNPs could be further evaluated in large scale as a potential human topical antifungal agent