Improved low pH bicelle system for orienting macromolecules over a wide temperature range

We have prepared and characterized a novel bicelle system composed of 1,2-di-O-dodecyl-sn-glycero-3-phos- phocholine (DIODPC) and 3-(chloramidopropyl)dimethylammonio-2-hydroxyl-1-propane sulfonate (CHAPSO). At the optimal DIODPC/CHAPSO molar ratio of 4.3:1, this medium becomes magnetically oriented from pH 6.5 down to pH 1.0. Unlike previously reported bicelle preparations, these bicelles are chemically stable at low pH and are capable of inducing protein alignment, as illustrated by the large residual dipolar couplings measured for rusticyanin from Thiobacillus ferrooxidans at pH 2.1. The DIODPC/CHAPSO system is particularly useful for measuring residual dipolar couplings of macromolecules that require very acidic conditions.     

Existence of a macrophyte-dominated clear water state over a very wide range of nutrient concentrations in a small shallow lake

Little Mere, a small shallow lake, has been monitored for four years, since its main source of nutrients (sewage effluent) was diverted. The lake has provided strong evidence for the persistence of a clear water state over a wide range of nutrient concentrations. It had clear water at extremely high nutrient concentrations prior to effluent diversion, associated with high densities of the large body-sized grazer, Daphnia magna, associated with low fish densities and fish predation. Following sewage effluent diversion in 1991, the nutrient concentrations significantly declined, the oxygen concentrations rose, and fish predation increased. The dominance of large body-sized grazers shifted to one of relatively smaller body-sized animals but the clear water state has been maintained. This is probably due to provision of refuges for grazers by large nymphaeid stands (also found prior to diversion). There has been a continued decrease in nutrient concentrations and expansion of the total macrophyte coverage, largely by submerged plants, following effluent diversion. The grazer community of Little Mere has also responded to this latter change with a decline in daphnids and increase in densities of weed-associated grazers. The presence of large densities of such open water grazers was the apparent main buffer mechanisms of the clear water state until 1994. The lake has, so far, maintained its clear water in the absence of such grazers. Thus, new buffer mechanisms appear to operate to stabilize the ecosystem. Little Mere appears to have shifted from previous top-down controlled clear water state to a bottom-up controlled clear water state.     

Thermotaxis and protoplasmic oscillations inPhysarum plasmodia analysed in a novel device generating stable linear temperature gradients

Summary The application of sublethal temperature gradients offers a simple, non-invasive means for in vivo studies of thermotaxis and other temperature-dependent processes in various organisms. Development, for instance, can be dramatically desynchronized, and the resulting development gradients allow to analyze physiological inter-dependencies between locally separated subsystems. For this purpose a simple device has been developed, by which a stable linear gradient of 8 °C/cm is established on an inert metal sheet with the aid of Peltier elements. The effects of linear temperature gradients on fusion, growth, and migration of plasmodia of the slime moldPhysarum polycephalum was filmed by 16 mm film time-lapse technique, and their local contraction—relaxation cycles analysed by multistrip kymography, which represents a graphic documentation of the spatio-temporal pattern of protoplasmic movements that occur along well-defined regions within the giant cell.Physarum plasmodia preferentially fuse, and grow, in the range of 24–26 °C. Different parts of a single macroplasmodium can simultaneously show positive and negative thermotaxis. The contraction—relaxation cycles generating the protoplasmic shuttle streaming within the network of veins essentially depend on local temperatures and are instantaneously desynchronized by the temperature gradient. Thus they cannot be controlled by a central pacemaker or an overall electric signal. However, there is a strong tendency to locally synchronize the various oscillation frequencies present within the giant cell if temperature differences do not exceed 2 °C.     

Cholesterol sulfate and calcium affect stratum corneum lipid organization over a wide temperature range

The main diffusion barrier for drugs penetrating through the skin is located in the intercellular lipid matrix in the upper layer of the skin, the stratum corneum (SC). The main lipid classes in the SC are ceramides (CER), free fatty acids (FFA) and cholesterol (CHOL). The lipids in SC are organized into two lamellar phases with periodicities of approximately 13 and 6 nm, respectively. Similar lipid organization has been found with equimolar CHOL:CER:FFA mixtures in SAXD studies performed at room temperature. However, one may conclude that the phase behavior of the mixtures is similar to that in SC only when the lipid organization of the lipid mixtures resembles that in SC over a wide temperature range. Therefore, in the present study, the organization of the lipid mixtures has been studied in a temperature range between 20 degrees and 95 degrees C. From these experiments it appeared that at elevated temperatures in equimolar CHOL:CER:FFA mixtures a new prominent 4.3 nm phase is formed between 35;-55 degrees C, which is absent or only weakly formed in intact human and pig SC, respectively. As it has been suggested that gradients of pH and cholesterol sulfate exist in the SC and that Ca(2+) is present only in the lowest SC layers, the effect of pH, cholesterol sulfate, and Ca(2+) on the lipid phase behavior has been investigated with lipid mixtures. Both an increase in pH from 5 (pH at the skin surface) to 7.4 (pH at the SC;-stratum granulosum interface) and the presence of cholesterol sulfate promote the formation of the 13 nm lamellar phase. Furthermore, cholesterol sulfate reduces the amount of CHOL that is present in crystalline domains, causes a shift in the formation of the 4.3 nm phase to higher temperatures, and makes this phase less prominent at higher temperatures. The finding that Ca(2+) counteracts the effects of cholesterol sulfate indicates the importance of a proper balance of minor SC components for appropriate SC lipid organization. In addition, when the findings are extrapolated to the in vivo situation, it seems that cholesterol sulfate is required to dissolve cholesterol in the lamellar phases and to stabilize SC lipid organization. Therefore, a drop in cholesterol sulfate content in the superficial layers of the SC is expected to destabilize the lipid lamellar phases, which might facilitate the desquamation process.     

An effective iodide formulation for killing Bacillus and Geobacillus spores over a wide temperature range

AIMS: To develop a sporicidal reagent which shows potent activity against bacterial spores not only at ambient temperatures but also at low temperatures. METHODS AND RESULTS: Suspension tests on spores of Bacillus and Geobacillus were conducted with the reagent based on a previously reported agent (N. Kida, Y. Mochizuki and F. Taguchi, Microbiology and Immunology 2003; 47: 279-283). The modified reagent (tentatively designated as the KMT reagent) was composed of 50 mmol l(-1) EDTA-2Na, 50 mmol l(-1) ferric chloride hexahydrate (FeCl(3).6H(2)O), 50 mmol l(-1) potassium iodide (KI) and 50% ethanol in 0.85% NaCl solution at pH 0.3. The KMT reagent showed significant sporicidal activity against three species of Bacillus and Geobacillus spores over a wide range of temperature. The KMT reagent had many practical advantages, i.e. activity was much less affected by organic substances than was sodium hypochlorite, it did not generate any harmful gas and it was stable for a long period at ambient temperatures. The mechanism(s) of sporicidal activity of the KMT reagent was considered to be based on active iodine species penetrating the spores with enhanced permeability of the spore cortex by a synergistic effect of acid, ethanol and generated active oxygen. CONCLUSIONS: The data suggest that the KMT reagent shows potent sporicidal activity over a wide range temperatures and possesses many advantages for practical applications. SIGNIFICANCE AND IMPACT OF THE STUDY: The results indicate development of a highly applicable sporicidal reagent against Bacillus and Geobacillus spores.     

MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.

Single-stranded DNAzyme-based Pb2+ fluorescent sensor that can work well over a wide temperature range

DNAzymes have become an excellent choice for sensing applications. Based on DNAzymes, three generations of Pb(2+) fluorescent sensors have been reported. In these sensors, two oligonucleotide strands (substrate strand and enzyme strand) were used, which not only increased the complexity of the detection system, but also brought some difficulties for the use of the sensors at elevated temperatures. To overcome this problem, a single-stranded DNAzyme-based Pb(2+) fluorescent sensor was designed by combining the substrate sequence and the enzyme sequence into one oligonucleotide strand. The intramolecular duplex structure of this single-stranded DNAzyme kept the fluorophore and the quencher, labeled at its two ends, in close proximity; thus the background fluorescence was significantly suppressed. Using this fluorescent sensor, Pb(2+) quantitation can be achieved with high sensitivity and high selectivity. In addition, the extraordinary stability of the intramolecular duplex structure could assure a low background fluorescence at high temperature, even if the number of complementary base pairs between the substrate sequence and the enzyme sequence was reduced, allowing the sensor to work well over a wide temperature range. Similar performances of the fluorescent sensor at 4, 25 and 37°C suggested that this sensor has a good ability to resist temperature fluctuations.     

Computer prediction of human thermoregulatory and temperature responses to a wide range of environmental conditions

A mathematical model for predicting human thermal and regulatory responses in cold, cool, neutral, warm, and hot environments has been developed and validated. The multi-segmental passive system, which models the dynamic heat transport within the body and the heat exchange between body parts and the environment, is discussed elsewhere. This paper is concerned with the development of the active system, which simulates the regulatory responses of shivering, sweating, and peripheral vasomotion of unacclimatised subjects. Following a comprehensive literature review, 26 independent experiments were selected that were designed to provoke each of these responses in different circumstances. Regression analysis revealed that skin and head core temperature affect regulatory responses in a non-linear fashion. A further signal, i.e. the rate of change of the mean skin temperature weighted by the skin temperature error signal, was identified as governing the dynamics of thermoregulatory processes in the cold. Verification and validation work was carried out using experimental data obtained from 90 exposures covering a range of steady and transient ambient temperatures between 5°C and 50°C and exercise intensities between 46 W/m² and 600 W/m². Good general agreement with measured data was obtained for regulatory responses, internal temperatures, and the mean and local skin temperatures of unacclimatised humans for the whole spectrum of climatic conditions and for different activity levels. Received: 20 November 2000 / Revised: 24 April 2001 / Accepted: 14 May 2001     

Circadian rhythms in the thermophilic cyanobacterium Thermosynechococcus elongatus: compensation of period length over a wide temperature range

Proteins derived from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, which performs plant-type oxygenic photosynthesis, are suitable for biochemical, biophysical, and X-ray crystallographic studies. We developed an automated bioluminescence real-time monitoring system for the circadian clock in the thermophilic cyanobacterium T. elongatus BP-1 that uses a bacterial luciferase gene set (Xl luxAB) derived from Xenorhabdus luminescens as a bioluminescence reporter gene. A promoter region of the psbA1 gene of T. elongatus was fused to the Xl luxAB gene set and inserted into a specific targeting site in the genome of T. elongatus. The bioluminescence from the cells of the psbA1-reporting strain was measured by an automated monitoring apparatus with photomultiplier tubes. The strain exhibited the circadian rhythms of bioluminescence with a 25-h period length for at least 10 days in constant light and temperature. The rhythms were reset by light-dark cycle, and their period length was almost constant over a wide range of temperatures (30 to 60 degrees C). Theses results indicate that T. elongatus has the circadian clock that is widely temperature compensated.     

In Vitro measurement of tissue impedance over a wide frequency range

Summary A simple method is described to determine the loci of the specific impedance of biological materialsin vitro. A waveform generator and a x-y-oscilloscope were used. With this setup impedance loci from 1 kHz to 6.4 MHz could be obtained. The error caused by the final input impedance of the amplifier was corrected mathematically. The loci of the specific impedance of centrifuged human erythrocytes and of rabbit brain cortex, liver and kidney were determined.     

Patterns of DNA methylation are indistinguishable in different individuals over a wide range of human DNA sequences.

Patterns of DNA methylation at 5'-CCGG-3' and 5'-GCGC-3' sequences were determined in about 570 kb, equivalent to about 0.02% of the human genome, by using HpaII and HhaI restriction endonucleases, respectively, and randomly selected cosmid clones of human DNA as hybridization probes. Many of these human DNA sequences were of the repetitive type. The DNAs from human lymphocytes, from a mixture of all blood cells or from several established human cell lines (HeLa, KB, 293, or DEV) were included in these analyses. In the segments of the human genome investigated, the patterns of DNA methylation were characterized by often completely or partly methylated 5'-CCGG-3' or by partly methylated 5'-GCGC-3' sequences. Even among individuals of different genetic origins (East-Asian or Caucasian), these patterns of DNA methylation proved indistinguishable by the method applied. The cytokine-dependent stimulation of human lymphocytes to replicate in culture did not affect the stability of these patterns. In the same DNA sequences from several human cell lines, much lower levels of DNA methylation were observed. In human cell lines some of the investigated sequences were unmethylated. The results presented lend credence to the notion that the human genome exhibits highly cell type-specific patterns of DNA methylation which are often indistinguishable among different individuals even of different genetic backgrounds.     

A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35 degrees C

Escherichia coli cells are the most commonly used host cells for large-scale production of recombinant proteins, but some proteins are difficult to express in E. coli. Therefore, we tested the nocardioform actinomycete Rhodococcus erythropolis, which grows at temperatures ranging from 4 to 35 degrees C, as an expression host cell. We constructed inducible expression vectors, where the expression of the target genes could be controlled with the antibiotic thiostrepton. Using these expression vectors, several milligrams of reporter proteins could be isolated from 1 liter of culture of R. erythropolis cells grown at a temperature range from 4 to 35 degrees C. Moreover, we successfully purified serum amyloid A1, NADH dehydorogenase 1 alpha subcomplex 4, cytochrome b5-like protein, apolipoprotein A-V, cathepsin D, pancreatic Rnase, and HMG-1 that are all difficult to express in E. coli. In the case of kallikrein 6, mouse deoxyribonuclease I and Kid1, which are also difficult to express in E. coli, the expression level of each protein increased when proteins were expressed at low temperature (4 degrees C). Based on these results, we conclude that a recombinant protein expression system using R. erythropolis as the host cell is superior to respective E. coli systems.     

Genomic compatibility occurs over a wide range of parental genetic similarity in an outcrossing plant

The theory of inbreeding and outbreeding suggests that there is a hump-shaped relationship between the genetic similarity of sexually reproducing parents and the performance of their offspring. Inbreeding depression occurs when genetic similarity is high, whereas hybrid breakdown is expected when genetic similarity is low. Between these extremes, the effect of genetic similarity on fitness is unclear. We studied the shape of this relationship by crossing 65 target genotypes of the clonal, self-incompatible Ranunculus reptans with partner genotypes spanning a broad scale of genetic similarity, ranging from crosses within populations to between-population crosses and hybridisation with a closely related species. Offspring were raised in outdoor tubs. Results revealed a quadratic relationship between parental genetic distance and offspring performance, with the clonal component of fitness more strongly hump-shaped than the sexual component. Optimal genetic similarity encompassed a broad range of within-population and between-population crosses. This pattern of genomic compatibility has important implications for the evolution of mating systems and mate choice.     

All three human ras genes are expressed in a wide range of tissues

We examined the expression of the ras gene family (Ha-ras, Ki-ras, N-ras) in human fetal tissues (14 week) and in several human tumor cell lines. Dot blot hybridization showed that the three ras genes were expressed in all of the samples analysed, with a range of expression between 10 and 180 molecules/cell. There was no correlation between levels of expression of ras genes and the type of ras gene activated in different tumor types.     

The gel-filtration behaviour of proteins related to their molecular weights over a wide range

1. Correlation between elution volume, V_e, and molecular weight was investigated for gel filtration of proteins of molecular weights ranging from 3500 (glucagon) to 820000 (α-crystallin) on Sephadex G-200 columns at pH7·5. 2. Allowing for uncertainties in the molecular weights, the results for most of the carbohydrate-free globular proteins fitted a smooth V_e–log(mol.wt.) curve. In the lower part of the molecular-weight range the results were similar to those obtained with Sephadex G-75 and G-100 gels. 3. V_e–log(mol.wt.) curves based on results with the three gels are taken to represent the behaviour of `typical' globular proteins, and are proposed as standard data for the uniform interpretation of gel-filtration experiments. 4. Some glycoproteins, including γ-globulins and fibrinogen, do not conform to the standard relationship. The effect of shape and carbohydrate content on the gel-filtration behaviour of proteins is discussed. 5. As predicted by the theoretical studies of other authors, correlation exists between the gel-filtration behaviour and diffusion coefficients of proteins. 6. The lower molecular-weight limit for complete exclusion of typical globular proteins from Sephadex G-200 varies with the swelling of the gel, but is usually >10⁶. 7. The concentration-dependent dissociation of glutamate dehydrogenase was observed in experiments with Sephadex G-200, and the sub-unit molecular weight estimated as 250000. The free sub-units readily lose enzymic activity. 8. Recognition of the atypical gel-filtration behaviour of γ-globulins necessitates an alteration to several molecular weights previously estimated with Sephadex G-100 (Andrews, 1964). New values are: yeast glucose 6-phosphate dehydrogenase, 128000; bovine intestinal alkaline phosphatase, 130000; Aerobacter aerogenes glycerol dehydrogenase, 140000; milk alkaline phosphatase, 180000.     

Adaptive advantages of myrmecochory: the predator-avoidance hypothesis tested over a wide geographic range

The predator‐avoidance hypothesis states that once released from the parent plant, myrmecochorous seeds are rapidly taken by ants to their nests, where they are protected from predators. Previous studies conducted to test this hypothesis have frequently neglected two major aspects necessary for its verification: 1) the influence of processes acting after the seed release and 2) the spatial evenness of such processes. Thus, large‐scale variations in the mechanisms acting beyond seed release, and possibly influencing seed escape from predators, remain poorly documented. Here, we present the results of a post‐dispersal seed‐removal experiment on the myrmecochorous herb Helleborus foetidus, aimed at verifing the predator‐avoidance hypothesis by considering two key post‐release aspects of seed fate: seed destination (dispersed or nondispersed) and seed burial (buried or not buried). Experiments were performed in four different regions in the Iberian Peninsula. After three days of exposure of seeds to the main predator (fieldmice Apodemus sylvaticus), ca 30% of the seeds were removed. Seed destination affected the proportion of seeds escaping predation, but the sign, magnitude and statistical significance of the effect varied among the geographical regions. In the southern region (Cazorla), seeds dispersed in ant nests or intermediate destinations suffered scarcely any predation, but seeds under reproductive‐age plants experienced losses ca 50%. Conversely, in the northern region (Caurel), seeds in nests suffered significantly greater losses than seeds under plants or intermediate destinations, suggesting that nests were especially unsafe destinations. Seed burial had a strong impact on seed escape from predators, and its effect was highly consistent among geographical regions. In view of the consistency of its effect at different spatial scales, seed burial was a more general mechanism for predation avoidance than seed relocation to ant nests, which was habitat‐ and/or ant‐species‐dependent. Our results thus only partially support the predator‐avoidance hypothesis for the evolution of myrmecochory.     

Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range.

The photocycle of bacteriorhodopsin and its thermodynamic parameters were studied in the pH range of 4.5-9. Measurements were performed at five different wavelengths (410, 500, 570, 610, and 650 nm), in the time interval 300 ns to 0.5 s, at six temperatures between 5 and 30 degreesC. Data were fitted to different photocycle models. The sequential model with reversible reactions gave a good fit, and the linear character of the Eyring plots was fulfilled. The parallel model with unidirectional reactions gave a poor fit, and the Eyring plot of the rate constants did not follow the expected linear behavior. When a parallel model with reversible reactions, which has twice as many free parameters as the sequential model, was considered, the quality of the fit did not improve and the Eyring plots were not linear. The sequential model was used to determine the thermodynamic activation parameters (activation enthalpy, entropy, and free energy) of the transitions and the free energy levels of the intermediates. pH dependence of the parameters revealed details of the transitions between the intermediates: the transitions M1 to M2 and N to O disclosed a large entropy increase, which could be interpreted as a loosening of the protein structure. The pH dependence of the energy levels explains the disappearance of intermediate O at high pH. A hypothesis is proposed to interpret the relation between the observed pKa of the photocycle energetics and the role of several amino acids in the protein.     

Quantification of gene expression over a wide range by the polymerase chain reaction.

We investigated the usefulness of the polymerase chain reaction (PCR) method for the relative quantification of gene expression using a simultaneously amplified sequence of beta-actin mRNA as an internal control for the target sequence of tax/rex mRNA of human T-cell leukemia virus type I. The PCR product of the internal control was reduced by delaying the addition of the primers for its sequence. The photostimulated luminescence of the bands was measured with a laser image analyzer, and the values were plotted against the cycle number. The cycle differences between the logarithmic phase of the curves for the target sequence and for beta-actin (delta cycle) showed a linear correlation with the initial concentration of the sample. This method is highly sensitive for evaluating gene expression over a wide range.