A theoretical study of the cis-syn pyrimidine dimers in the gas phase and water cluster and a tautomer-bypass mechanism for the origin of UV-induced mutations

A quantum mechanical study of all cis-syn cyclobutane pyrimidine photodimers including the normal and rare tautomeric forms of bases has been performed using the ab initio method at HF/6-31G(d.p), MP2(fc)//HF/6-31G(d,p) and MP2(fc)/6-31G(d,p) levels. A puckering angle of the cyclobutyl ring and twist angle of pyrimidine rings with respect to each other is well described by these calculations. It is predicted that in the gas phase all photodimers containing the rare imino form of cytosine are more stable than those containing its normal form. The Monte Carlo simulations show that the dimer containing the imino form of cytosine is more stabilized by water cluster than that containing its amino forms. The possible biological significance stems from the fact that the cytosine in the dimer directs the incorporation of adenine in the complementary strand during replicative bypass. Data obtained point to the cytosine tautomerism as a possible mechanism for the origin of UV-induced mutation.     

Azaguanine: A Theoretical Study of Its Tautomerism and Protonation in the Gas Phase and Aqueous Solution

The tautomerism and protonation of 8-azaguanine (azaG) have been studied by means of ab initio methods, both in the gas phase and in aqueous solution. An elimination procedure to choose the most stable tautomeric forms, based on AM1 and HF/6–31G* energies, has been applied. Tautomers azaG(1,9), azaG(1,7) and azaG(9,15) have been selected and their energies calculated at MP2/6–311++G**//HF/6–31G* level. Self-consistent reaction field IPCM, based on polarizable continuum model (PCM), has been applied to study the solvent effects. The stability order in the gas phase is azaG(1,7) = azag(1,9) > azaG(9,15), whereas in solution the order becomes azaG(1,7) > azaG(1,9) > azaG(9,15), the latter being just 0.76 kcal/mol over azaG(1,7). The calculations of proton affinities allowed to unambiguously determine the preferred sites of protonation of these species.     

The Role of Pyrimidine Dimers as Premutagenic Lesions: A Study of Targeted VS. Untargeted Mutagenesis in the lacI Gene of ESCHERICHIA COLI

We have employed conjugal transfer of an F' lac episome to examine targeted and untargeted mutagenesis in the lacI gene of Escherichia coli and to determine the relative importance of pyrimidine dimers as premutational UV lesions compared to (6-4) photoproducts that also may have a mutational role. This conjugal system allowed us to assess the premutagenic role of UV lesions independently from any role as inducers of SOS functions. F' DNA was transferred to an SOS-induced recipient strain from: unirradiated donor cells, UV-treated donor cells or donor cells that were irradiated and then exposed to photoreactivating light. The results indicate that SOS-related, untargeted events may account for as much as one-third of the nonsense mutations (i.e., base substitutions) recovered after undamaged F' DNA is transferred to UV-irradiated recipients. When the donor strain also is irradiated, in excess of 90% of the mutations detected following conjugation appear to be targeted. Photoreactivation of the UV-treated donors cells, prior to F' transfer to the SOS-induced recipient strain, demonstrated that in this experimental system virtually all recovered UV-induced mutations are targeted by photoreactivable lesions. We presume that these lesions are pyrimidine dimers because (6-4) photoproducts are not photoreactivable.     

Influence of the Distributed Phase of Gas Bubbles on a Pulsed Electrical Discharge in Water

The development of a pulsed electrical discharge in water with vapor–air microbubbles, the volume distribution of which in water is close to uniform, has been studied experimentally. The presence of volumetric microbubbles with an average diameter of ~50 μm and a bulk gas content of no more than 1% does not change the thermal mechanism of the development of the discharge in water with a conductivity of ~300 μS/cm at overvoltages of 1–1.5, the minimum breakdown voltage being ~9 kV. Under these conditions, the determining role is played by the surface bubbles, which change the observed mechanism of the discharge development. The discharge is initiated in the surface bubbles simultaneously on both electrodes. The growth of the cathode channel at a velocity of ~60 m/s leads to the closure of the 1-cm-long gap during a time of ~160 μs.     

A Theoretical Study of Pulmonary Capillary Gas Exchange and Venous Admixture

A model of pulmonary capillary gas exchange and venous admixture is presented and the inclusion of this model into a model of the entire respiratory system is discussed. Partial pressure and concentration gradients for nitrogen, helium, oxygen, and carbon dioxide are predicted. The cases of breathing room air and 10% oxygen are studied. In both of these studies the Bohr and Haldane effects are included, and the “physiological” dissociation curves of oxygen and carbon dioxide are predicted for the normal case as blood flows from the venous blood end of the capillary to the arterial blood end. Venous admixture effects are also calculated for both of these cases. The effects of emphysema, pulmonary congestion, and altered cardiac function on the gradients are studied.     

Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity

The development of resistance to different drugs remains a major problem for a wide range of infections. In particular, combinations of specific mutations, which individually demonstrate no effect, exhibit significant cooperativity. Here we show that changes to the energy of ligand binding in different resistant HIV-1 proteases are correlated with the creation of water binding sites in the active site. This correlation is conserved across two drugs (ritonavir and lopinavir). We propose that individual mutations induce changes in flap packing that are insufficient to allow water binding but in combination allow access, leading to the observed cooperative resistance.     

Hollandite as a Functional and Structural Model for the Biological Water Oxidizing Complex: Manganese-Calcium Oxide Minerals as a Possible Evolutionary Origin for the CaMn4 Cluster of the Biological Water Oxidizing Complex

Oxygen evolution was observed upon mixing either hollandite, which has been proposed as a structural model for the biological water oxidizing complex, or hausmannite with an aqueous solution of cerium (IV) ammonium nitrate. Oxygen evolution from water during irradiation with visible light (λ > 400 nm) was also observed upon adding either hollandite or hausmannite to an aqueous solution containing tris (2,2′-bipyridyl)ruthenium(II) chloride and chloro pentaammine cobalt(III) chloride in acetate buffer. These experiments showed that hollandite is a good catalyst for oxygen evolution in presence of cerium (IV) ammonium nitrate or tris (2,2′-bipyridyl)ruthenium (III). Thus, hollandite is not only a structural but also a functional model for the biological water oxidizing complex. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.     

微泡对气体交换影响的理论研究

依据菲克第一定律、玻意耳定律及道尔顿气体分压定律,建立微泡内外气体交换的数学模型。通过理论推导和计算机模拟,研究微泡在不同条件下对机体的肺部、动脉系统及其周围组织等不同部位微循环中气体交换的影响。理论分析结果显示,O2、CO2及N2在三个部位都呈现为由内向外的弥散过程,且在正常呼吸条件下,超声造影剂微泡不会对周围组织微循环的气体交换产生有效的生理作用。而在吸氧35%或70%的条件下,微泡的携氧量明显增加,对三个部位局部周围组织微循环的气体交换产生一定影响。     

A Gas Lift Bioreactor for Removal of Contaminants from the Vapor Phase

The cometabolic degradation of trichloroethylene (TCE) as a vapor by two aromatic-metabolizing pseudomonads was evaluated in an airlift reactor. These microorganisms were able to degrade 90 to 95% of TCE in air at concentrations at the reactor inlet of 300 to 4,000 μg/liter. Although exposure of the cells to high inlet concentrations of TCE (4 mg/liter) caused a decline in enzyme-specific activity and TCE removal efficiency, this loss in activity could be prevented or delayed by increasing the rate of cosubstrate addition. Under the appropriate operating conditions, the microorganisms were able to degrade even high concentrations of TCE and activity of the cells in the reactor could be maintained for periods of at least 2 weeks.     

A Population-Based Study of Autosomal-Recessive Disease-Causing Mutations in a Founder Population

The decreasing cost of whole-genome and whole-exome sequencing has resulted in a renaissance for identifying Mendelian disease mutations, and for the first time it is possible to survey the distribution and characteristics of these mutations in large population samples. We conducted carrier screening for all autosomal-recessive (AR) mutations known to be present in members of a founder population and revealed surprisingly high carrier frequencies for many of these mutations. By utilizing the rich demographic, genetic, and phenotypic data available on these subjects and simulations in the exact pedigree that these individuals belong to, we show that the majority of mutations were most likely introduced into the population by a single founder and then drifted to the high carrier frequencies observed. We further show that although there is an increased incidence of AR diseases overall, the mean carrier burden is likely to be lower in the Hutterites than in the general population. Finally, on the basis of simulations, we predict the presence of 30 or more undiscovered recessive mutations among these subjects, and this would at least double the number of AR diseases that have been reported in this isolated population.     

A Temporal Mechanism for Generating the Phase Precession of Hippocampal Place Cells

The phase relationship between the activity of hippocampal place cells and the hippocampal theta rhythm systematically precesses as the animal runs through the region in an environment called the place field of the cell. We present a minimal biophysical model of the phase precession of place cells in region CA3 of the hippocampus. The model describes the dynamics of two coupled point neurons—namely, a pyramidal cell and an interneuron, the latter of which is driven by a pacemaker input. Outside of the place field, the network displays a stable, background firing pattern that is locked to the theta rhythm. The pacemaker input drives the interneuron, which in turn activates the pyramidal cell. A single stimulus to the pyramidal cell from the dentate gyrus, simulating entrance into the place field, reorganizes the functional roles of the cells in the network for a number of cycles of the theta rhythm. In the reorganized network, the pyramidal cell drives the interneuron at a higher frequency than the theta frequency, thus causing a systematic precession relative to the theta input. The frequency of the pyramidal cell can vary to account for changes in the animal's running speed. The transient dynamics end after up to 360 degrees of phase precession when the pacemaker input to the interneuron occurs at a phase to return the network to the stable background firing pattern, thus signaling the end of the place field. Our model, in contrast to others, reports that phase precession is a temporally, and not spatially, controlled process. We also predict that like pyramidal cells, interneurons phase precess. Our model provides a mechanism for shutting off place cell firing after the animal has crossed the place field, and it explains the observed nearly 360 degrees of phase precession. We also describe how this model is consistent with a proposed autoassociative memory role of the CA3 region.     

A Theoretical Study of Single-Cell Electroporation in a Microchannel

Electroporation of a single cell in a microchannel was studied. The effects of electrical (e.g., strength of the electric pulse) and geometrical (e.g., microchannel height, electrode size and position) parameters on cell membrane permeabilization were investigated. The electrodes were assumed to be embedded in the walls of the microchannel; the cell was suspended between these two electrodes. By keeping the electric pulse constant, increasing the microchannel height reduces the number and the radius of the biggest nanopores, as well as the electroporated area of the cell membrane. If the width of the electrodes is bigger than the cell diameter, the transmembrane potential will be centralized and have a sinusoidal distribution around the cell if nanopores are not generated. As the width of the electrode decreases and becomes smaller than the cell diameter, the local transmembrane potential decreases; in the nonelectroporative area, the transmembrane potential distribution deviates from the sinusoidal behavior; the induced transmembrane potential also concentrates around the poles of the cell membrane (the nearest points of the cell membrane to the electrodes). During cell membrane permeabilization, the biggest nanopores are initially created at the poles and then the nanopore population expands toward the equator. The number of the created nanopores reaches its maximal value within a few microseconds; further presence of the electric pulse may not influence the number and location of the created nanopores anymore but will develop the generated nanopores. Strengthening the electric pulse intensifies the size and number of the created nanopores as well as the electroporated area on the cell membrane.     

Evolution of a New Gene Substituting for the leuD Gene of Salmonella typhimurium: Origin and Nature of supQ and newD Mutations

The second specific enzyme in the biosynthesis of leucine, α-isopropylmalate isomerase, is coded for by two genes, leuC and leuD. Leucine auxotrophs carrying mutations in the leuD gene (including deletions of the entire leuD gene) revert to leucine prototrophy by secondary mutations at the locus supQ, which is located in the proline region of the chromosome. The mechanism of the supQ function is explained by the following model. The supQ gene and an additional gene, newD, code for two different subunits of a multimeric enzyme, whose normal function is yet to be determined. The newD gene protein is able, without genetic alterations, to form an active complex with the leuC protein, thus replacing the nonfunctional or missing leuD protein and restoring leucine prototrophy. The newD protein has, however, a higher affinity for the supQ protein than for the leuC protein; therefore, mutations in the supQ gene are needed to make sufficient amounts of the newD protein available. The following gene order has been established: gpt-proB-proA-ataA-supQ-newD. Different supQ mutations have been identified, i.e., insertion in the supQ gene, point mutations, and deletions of various extent. Some deletions remove the P22 phage attachment site ataA. Other supQ deletions are simultaneously Pro⁻, because they extend into the proA or proA and proB genes; some extend even further, i.e., into the gpt gene (guanine phosphoribosyl transferase). Mutations in the newD gene caused renewed leucine auxotrophy in leuD supQ mutant strains. One newD mutation causes a temperature-sensitive Leu⁺ phenotype. Alternate models for the supQ-newD interactions are discussed.     

紫外诱变菌降解菜籽饼粕中粗蛋白的实验研究

采用紫外照射法对原始菌株进行诱变和筛选,得到一株降解饼粕中粗蛋白能力较强的变异菌株UV—A,能使饼粕中粗蛋白的含量降到15．46％,是原始菌株的1．4倍。把该变异菌株接入到装有12．5kg菜籽饼粕的40L塑料箱内进行固体发酵,发现饼粕中粗蛋白的含量降解到8．9％。并通过正交设计试验确定变异菌株UV—A的培养条件为：NaCl5％,温度30℃,pH7．0,培养时间48h,其中温度对其影响最大。