Parameters Effects Evaluation of Microbial Strengthening of Sandy Soils in Mixing Experiments Using Taguchi Methodology

The effects of experimental parameters including soil type, curing duration, inoculum size, and biomass and nutrients concentration on soil strengthening due to calcite precipitation by Sporosarcina pasteurii PTCC 1645 were investigated. The laboratory-scale mixing experiments on remolded samples were designed by the Taguchi method. Soil type proved to be the most incorporating factor, followed by curing time and nutrient concentration. The main effect and the interactions of the parameters were presented and the optimal conditions were obtained. This suggests the importance of local conditions including soil type on any future large-scale, in situ application.     

Human erythrocyte flickering: temperature,ATP concentration,water transport,and cell aging,plus a computer simulation

Images of human erythrocytes from a healthy donor were recorded under differential interference contrast (DIC) microscopy; they were acquired rapidly (~336 Hz) and the intensity of the centermost pixel of each cell was recorded for ~60 s (20,000 values). Various techniques were used to analyze the data, including detrended fluctuation analysis (DFA) and multiscale entropy (MSE); however, power spectrum analysis was deemed the most appropriate for metrifying and comparing results. This analysis was used to compare cells from young and old populations, and after perturbing normal conditions, with changes in temperature, adenosine triphosphate (ATP) concentration (using NaF, an inhibitor of glycolysis, and α-toxin, a pore-forming molecule used to permeabilize red cells to ATP), and water transport rates [using glycerol, and p-chloromercuriphenylsulfonic acid (pCMBS) to inhibit aquaporins, AQPs]. There were measurable differences in the membrane fluctuation characteristics in populations of young and old cells, but there was no significant change in the flickering time series on changing the temperature of an individual cell, by depleting it of ATP, or by competing with the minor water exchange pathway via AQP3 using glycerol. However, pCMBS, which inhibits AQP1, the major water exchange pathway, inhibited flickering in all cells, and yet it was restored by the membrane intercalating species dibutyl phthalate (DBP). We developed a computer model to simulate acquired displacement spectral time courses and to evaluate various methods of data analysis, and showed how the flexibility of the membrane, as defined in the model, affects the flickering time course.     

The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

Upon ATP binding, myosin motor protein is found in two alternative conformations, prerecovery state M* and postrecovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in prerecovery state to “down” position in postrecovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force‐generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487, and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. Proteins 2012; © 2012 Wiley Periodicals, Inc.     

A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations

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Computer simulation of synchronization of Na/K pump molecules

The behavior of Na/K pump currents when exposed to an oscillating electric field is studied by computer simulation. The pump current from a single pump molecule was sketched based on previous experimental results. The oscillating electric field is designed as a symmetric, dichotomous waveform varying the membrane potential from −30 to −150 mV around the membrane resting potential of −90 mV. Based on experimental results from skeletal muscle fibers, the energy needed to overcome the electrochemical potentials for the Na and K-transports are calculated in response to the field’s two half-cycles. We found that a specially designed oscillating electric field can eventually synchronize the pump molecules so that all the individual pumps run at the same pumping rate and phase as the field oscillation. They extrude Na ions during the positive half-cycle and pump in K ions during the negative half-cycle. The field can force the two ion-transports into the corresponding half-cycles, respectively, but cannot determine their detailed positions. In other words, the oscillating electric field can synchronize pumps in terms of their pumping loops but not at a specific step in the loop. These results are consistent with our experimental results in measurement of the pump currents.     

High resolution methylation analysis of the HoxA5 regulatory region in different somatic tissues of laboratory mouse during development

Homeobox genes encode a group of DNA binding regulatory proteins whose key function occurs in the spatial-temporal organization of genome during embryonic development and differentiation. The role of these Hox genes during ontogenesis makes it an important model for research. HoxA5 is a member of Hox gene family playing a central role during axial body patterning and morphogenesis. DNA modification studies have shown that the function of Hox genes is partly governed by the methylation-mediated gene expression regulation. Therefore the study aimed to investigate the role of epigenetic events in regulation of tissue-specific expression pattern of HoxA5 gene during mammalian development. The methodology adopted were sodium bisulfite genomic DNA sequencing, quantitative real-time PCR and chromatin-immunoprecipitation (ChIP). Methylation profiling of HoxA5 gene promoter shows higher methylation in adult as compared to fetus in various somatic tissues of mouse being highest in adult spleen. However q-PCR results show higher expression during fetal stages being highest in fetal intestine followed by brain, liver and spleen. These results clearly indicate a strict correlation between DNA methylation and tissue-specific gene expression. The findings of chromatin-immunoprecipitation (ChIP) have also reinforced that epigenetic event like DNA methylation plays important role in the regulation of tissue specific expression of HoxA5.     

增加降水对荒漠短命植物当年牧草生长及群落结构的影响

通过模拟降水增加试验研究了古尔班通古特荒漠常见短命植物盖度、密度及产量对水分输入量增加的响应.结果表明:尖喙牻牛儿苗、弯果胡卢巴、角果藜、琉苞菊、条叶庭芥及囊果苔草6种牧草生物量总和占总生物量的60%以上,是荒漠草原的优势牧草植物;供水量增加显著促进了角果藜、尖喙牻牛儿苗、弯果胡卢巴、条叶庭芥和琉苞菊5种牧草植物的个体生长;在自然降水的基础上,增加40mm和80mm供水使这5种植物生物产量比对照增加86%～230%.供水增加后,6种重要牧草对整个群落的生物贡献比例发生很大变化,只有角果藜和尖喙牻牛儿苗的贡献比例规律性增加,分别比对照增加了58%和11%,表明2种植物对供水增加的环境变化适应能力强;供水量增加促进了弯果胡芦巴、尖喙牻牛儿苗和角果藜3种植物N、P和K养分的吸收量;与此同时,供水量增加也显著提高了荒漠短命植物的密度和盖度.在降水增加的背景下,古尔班通古特沙漠南缘荒漠短命植物群落结构发生改变,植被盖度和群落净初级生产力提高,这对于防风固沙、稳定沙面,增加荒漠草原载畜能力有着积极的意义.     

The evolution of premating isolation: local adaptation and natural and sexual selection against hybrids

Although reinforcement is ostensibly driven by selection against hybrids, there are often other components in empirical cases and theoretical models of reinforcement that may contribute to premating isolation. One of these components is local adaptation of a trait used in mate choice. I use several different comparisons to assess the roles that local adaptation and selection against hybrids may play in reinforcement models. Both numerical simulations of exact recursion equations and analytical weak selection approximations are employed. I find that selection against hybrids may play a small role in driving preference evolution in a reinforcement model where the mating cue is separate from loci causing hybrid incompatibilities. When females have preferences directly for purebreds of their own population, however, selection against hybrids can play a large role in premating isolation evolution. I present some situations in which this type of selection is likely to exist. This work also illustrates shortfalls of using a weak selection approach to address questions about reinforcement.