Detection of an abasic site in RNA with stem-loop DNA beacons: application to an activity assay for Ricin Toxin A-Chain

The catalytic ability of Ricin Toxin A-Chain (RTA) to create an abasic site in a 14-mer stem-tetraloop RNA is exploited for its detection. RTA catalyzes the hydrolysis of the N-glycosidic bond of a specific adenosine in the GAGA tetraloop of stem-loop RNA. Thus, a 14-mer stem-loop RNA substrate containing an intact “GAGA” sequence can be discriminated from the product containing an abasic “GabGA” sequence by hybridization with a 14-mer DNA stem-loop probe sequence and following the fluorescent response of the heteroduplexes. Three DNA beacon probe designs are described. Beacon 1 probe is a stem-loop structure and has a fluorophore and a quencher covalently linked to the 5′- and 3′-ends. In this format the probe–substrate heteroduplex gives a fluorescent signal while the probe–product one remains quenched. Beacon 2 is a modified version of 1 and incorporates a pyrene deoxynucleoside for recognition of the abasic site. In this format both the substrate and product heteroduplexes give a fluorescent response. Beacon 3 utilizes a design where the fluorophore is on the substrate RNA sequence at its 5′-end while the quencher is on the probe DNA sequence at its 3′-end. In this format the fluorescence of the substrate–probe heteroduplex is quenched while that of the product–probe one is enhanced. The lower limit of detection with beacons is 14 ng/mL of RTA.     

Effect of 0.25 N sodium chloride treatment on DNA denaturation in situ in thymus lymphocytes

Extraction of cells with 0.25 N NaCl changes the profile of DNA denaturation in situ. The portion of DNA denaturing at lower temperatures (“thermosensitive” fraction) shows increased sensitivity to heat following salt extraction while the “thermoresistant” DNA fraction is further stabilized. The results suggest that proteins extractable with 0.25 N NaCl while providing local counterions for DNA phosphates of the “thermosensitive” DNA fraction also decrease the strength of DNA-histone interactions within the “thermoresistant” fraction.     

Time-Qualified Reference Limits (Chronodesms) for 24-Hour Blood Pressure Values: Classical and Bayesian

Background - This paper is a concrete example of the problems raised by the need of constructing the time-qualified reference limits (chronodesms) for blood pressure (BP), in order to clinically estimate the hemodynamic parameter in its intrinsic nychtohemeral variability. Methods - Assuming that the noninvasive ambulatory BP monitoring (ABPM) is the eligible technique for this need, it must be realized that the BP chronodems may be of two types, depending on the sample being used for their calculation. The first type may be regarded as “ a priori ” because of the fact that they are derived by a sample of normotensive subjects who are unavoidably recruited via “ causal ” sphygmomanometric measurements and reclassified as normotensive by comparing their ABPM to the fixed reference limits (monodesms) given by WHO (monodiagnosis). Therefore, the “ a priori ” BP chonodesms are by principle derived by subjects who could not be correctly classified as normotensive, their ABPM being not tested versus the time-varying physiological limits. The second type may regarded as “ a posteriori ” in virtue of the fact that they may be constructed on a sample which contemplates the previous subjects who result to be true normotensive via the reassessment of their ABPM versus the “ a priori ” BP chronodesms (chronodiagnosis). The “ a posteriori ” chronodesms may be regarded as biometrically reliable, whether the sample for their construction is additionally constituted by those subjects of the local population who have been erroneously monodiagnosed as hypertensive, while they result to be true normotensive via the chronodiagnostic comparison of their ABPM versus the “ a priori ” BP chronodesms. Results - The biometric reliability of the “ a posteriori ” BP chronodems is demonstrated by the fact that their upper limits are statistically significantly less pronounced due to the fact that they are provided by a sample which has been depured by the falsely monodiagnosed normotensives. Conclusions - The “ a posteriori ” BP upper chronodesms are the time-qualified reference limits which should be used in clinical practice for the chronodiagnosis of hypertension.     

The role of dynamic stimulation pattern in the analysis of bistable intracellular networks

Bistable systems play an important role in the functioning of living cells. Depending on the strength of the necessary positive feedback one can distinguish between (irreversible) “one-way switch” or (reversible) “toggle-switch” type behavior. Besides the well- established steady-state properties, some important characteristics of bistable systems arise from an analysis of their dynamics. We demonstrate that a supercritical stimulus amplitude is not sufficient to move the system from the lower (off-state) to the higher branch (on-state) for either a step or a pulse input. A switching surface is identified for the system as a function of the initial condition, input pulse amplitude and duration (a supercritical signal). We introduce the concept of bounded autonomy for single level systems with a pulse input. Towards this end, we investigate and characterize the role of the duration of the stimulus. Furthermore we show, that a minimal signal power is also necessary to change the steady state of the bistable system. This limiting signal power is independent of the applied stimulus and is determined only by systems parameters. These results are relevant for the design of experiments, where it is often difficult to create a defined pattern for the stimulus. Furthermore, intracellular processes, like receptor internalization, do manipulate the level of stimulus such that level and duration of the stimulus is conducive to characteristic behavior.     

"Live memory" of the cell, the other hereditary memory of living systems

We propose to designate by the term “live memory” of the cell, the cytoplasmic memory. This phenomenon consists of non-genetic memory, but nevertheless includes transmission function, which may be “hereditary” via the ovum, from mother cell to daughter cell, or simply within the same cell from instant t to instant t + 1. To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.     

Mechanisms of nuclear localization of the progesterone receptor

Deletion mutants of the rabbit progesterone receptor were used to identify two major mechanisms of its nuclear localization. A putative signal sequence, homologous to that of the SV40 large T antigen, was localized around amino acids 638–642 and was shown to be constitutively active. When amino acids 638–642 were deleted, the receptor became cytoplasmic but could be shifted into the nucleus by the addition of hormone (or antihormone), it was almost fully active. A second putative nuclear localization signal is located in the DNA binding domain activated either through ligand binding or through production of constitutive receptor. By deleting epitopes recognized by monoclonal antibodies, it was possible to follow different receptor mutants inside the same cells. In the absence of ligand the receptor was transferred into the nucleus as a monomer. After administration of hormone (or antihormone) a “cytoplasmic” monomer was transferred into the nucleus through interaction with a “nuclear” monomer. These interactions occurred through the steroid binding domains of both monomers.     

A nanoparticle label/immunochromatographic electrochemical biosensor for rapid and sensitive detection of prostate-specific antigen

We present a nanoparticle (NP) label/immunochromatographic electrochemical biosensor (IEB) for rapid and sensitive detection of prostate-specific antigen (PSA) in human serum. This IEB integrates the immunochromatographic strip with the electrochemical detector for transducing quantitative signals. The NP label, made of CdSe@ZnS, serves as a signal-amplifier vehicle. A sandwich immunoreaction was performed on the immunochromatographic strip. The captured NP labels in the test zone were determined by highly sensitive stripping voltammetric measurement of the dissolved metallic component (cadmium) with a disposable-screen-printed electrode, which is embedded underneath the membrane of the test zone. Several experimental parameters (e.g., immunoreaction time, the amount of anti-PSA-NP conjugations applied) and electrochemical detection conditions (e.g., preconcentration potential and time) were optimized using this biosensor for PSA detection. The analytical performance of this biosensor was evaluated with serum PSA samples according to the “figure-of-merits” (e.g., dynamic range, reproducibility, and detection limit). The results were validated with enzyme-linked immunosorbent assay (ELISA) and showed high consistency. It is found that this biosensor is very sensitive with the detection limit of 0.02 ng mL⁻¹ PSA and is quite reproducible (with a relative standard deviation (R.S.D.) of 6.4%). This method is rapid, clinically practical, and less expensive than other diagnostic tools for PSA; therefore, this IEB coupled with a portable electrochemical analyzer shows great promise for simple, sensitive, quantitative point-of-care testing of disease-related protein biomarkers.     

Behavioral evaluation and demographic information in the assessment of aggressiveness in shelter dogs

Behavioral evaluations of 2017 shelter dogs were used for identifying dogs with aggressive tendencies and for predicting post-adoption behavior problems. Associations between failure of the behavioral evaluation and demographic factors (age, breed, and sex) and the dog's behavioral history, evaluated by logistic regression, were highly significant (P < 0.0005), except for “old” dogs (age > 72 months). Dogs that failed the behavior evaluation were not placed for adoption; therefore it was not possible to study prospectively the capability of behavioral evaluation to predict future aggressiveness in these dogs. Instead we developed tests for classifying dogs as aggressive or not aggressive based on their demographic factors and behavior evaluation outcomes. The results were compared retrospectively to the dogs’ known behavioral histories, which were obtained at intake to the shelter. This allowed estimation of the sensitivity, specificity, and accuracy of the classification tests. The most significant postdictor (i.e., “retrospective predictor”) of aggressiveness was failure of the behavioral evaluation (odds ratio 11.83, P < 0.0005). Among dogs that passed the behavioral evaluation, classification as “unsocial” by the behavioral evaluation was associated with nonaggressive behavior problems reported at 6-month follow-up (P = 0.005), and classification as “borderline” was associated with return to the shelter for aggressive behavior (P = 0.028). Behavioral evaluations reduced the rate of returns of adopted dogs from 19% in the year prior to their institution to 14% (P = 0.001) during the 2-year study period. Returns for aggression were reduced from 5% to 3.5% (P = 0.05), with many fewer incidents of serious aggression. The majority of dogs (86%) that failed the behavioral evaluation failed multiple component tests, indicating general aggressive tendencies in these dogs. Together with demographic information and behavioral history, behavioral evaluations can help to improve decisions regarding the disposition of shelter dogs.     

A stochastic model for chemosensory cell movement: application to neutrophil and macrophage persistence and orientation

Two central features of leukocyte chemosensory movement behavior demand fundamental theoretical understanding. In uniform concentrations of chemoattractant, these cells exhibit a persistent random walk, with a characteristic “persistence time” between significant changes in direction. In chemoattractant concentration gradients, they demonstrate a biased random walk, with an “orientation bias” characterizing the fraction of cells moving up the gradient. A coherent picture of cell-movement responses to chemoattractant requires that both the persistence time and the orientation bias be explained within a unifying framework. In this paper we offer the possibility that “noise” in the cellular signal perception/response mechanism can simultaneously account for these two key phenomena. In particular, we report on a stochastic mathematical model for cell locomotion based on kinetic fluctuations in chemoattractant receptor binding. This model proves to be capable of stimulating cell paths similar to those observed experimentally for two cell types examined to date: neutrophils and alveolar macrophages, under conditions of uniform chemoattractant concentrations as well as chemoattractant concentration gradients. Further, this model can quantitatively predict both cell persistence time and dependence of orientation bias on gradient size. The model also successfully predicts that an increase in persistence time is associated with a decrease in orientation for typical system parameter values, as is observed for alveolar macrophages in comparison to neutrophils. Thus, the concept of signal “noise” can quantitatively unify the major characteristics of leukocyte random motility and chemotaxis. The same level of noise large enough to account for the observed frequency of turning in uniform environments is simultaneously small enough to allow for the observed degree of directional bias in gradients. This suggests that chemosensory cell movement behavior may be based on a “usefully” imperfect integrated signal response system, which allows both random and directed searches under appropriate conditions.     

A pilot experiment on a method for evaluating acceptability of a daylit luminous environment

1. 1. We propose a hierarchical model as a hypothesis to evaluate comfort in lighting environments.

2. 2. The model consists of physical quantities such as stimuli, and visual sensations as the first response, and then overall evaluation.

3. 3. A pilot experiment in a side-lit classroom usng 147 subjects was made to examine this model.

4. 4. It was found that in the side-lit classroom the most effective answers for discrimination between “acceptable” and “not acceptable” were “the surface of desk was not considered dark” and “not to experience any reflectance of lighting on the sheet of paper on which they wrote”.

5. 5. Moreover all of the effective items relate to the task area, namely desk and blackboard, and this meant that subjects gave priority to workability in the classroom.

Development of a fast DNA-DNA hybridization method based on melting profiles in microplates

DNA-DNA hybridization is still the “gold standard” for the genotypic delineation of bacterial species. However, it is not widely used because traditional DNA-DNA hybridization techniques are rather time-consuming and not easy to perform in routine laboratories. In the present study, DNA of reference strains was digested with Sau3A, ligated with linker oligonucleotides S1/2 and in vitro amplified. The amplified DNA fragments were immobilized on MaxiSorb 96-well plates. DNA isolated from target strains was also digested with Sau3A, ligated with linker oligonuleotides P1/2 and in vitro amplified in the presence of digoxygenin modified dUTP. The labeled amplificate was hybridized to the immobilized reference DNA under isothermal conditions. Thermal denaturation curves of the DNA-DNA hybrids were obtained by using washing solutions of increasing stringency. Remaining hybrids were colorimetrically detected with anti-digoxygenin-horseradish peroxidase anti-bodies. The new method was validated with strains of the genus Pedioccocus for which DNA-DNA similarities have also been determined by the filter hybridization method. In addition, DNA-DNA hybridizations were performed with genotypically defined Enterobacter species.     

Temperature profiles, and the effect of sleep on them, in relation to morningness-eveningness in healthy female subjects

There were 15 healthy female subjects, differing in their position on the “morningness-eveningness” scale, studied for 7 consecutive days, first while living a sedentary lifestyle and sleeping between midnight and 08:00 and then while undergoing a “constant routine.” Rectal temperature was measured at regular intervals throughout this time, and the results were subjected to cosinor analysis both before and after “purification” for the effects of physical activity. Results showed that there was a phase difference in the circadian rhythm of core temperature that was associated with the morningness score, with calculations that “morning types” would be phased earlier than “evening types” by up to about 3h. This difference in phase (which was also statistically significant when the group was divided by a median split into a “morning group” and an “evening group”) could not be attributed to effects of waking activity and existed in spite of the subjects keeping the same sleep-wake schedule. Moreover, it persisted when the subjects' data had been purified and when the data were obtained from the constant routine. That is, there was an endogenous component to this difference in phase of the core temperature. The morning group also showed a greater fall of core temperature during sleep; this was assessed in two ways, the main one being a comparison of constant routine and nychthemeral data sets after correction for any effects of activity. Even though the morning group was sleeping at a later phase of their circadian temperature rhythm than was the evening group, neither group showed a fall of temperature due to sleep that varied with time elapsed since the temperature acrophase. It is concluded that another factor that differs between morning and evening types is responsible for this difference. (Chronobiology International, 18(2), 227-247, 2001)     

Interim Report of the Committee on Histologic Mounting Media: Resinous Media

The Fisher “Permount” naphthalene polymer, the Hartman Leddon “H.S.R.” terpene polymer resin, a Monsanto polystyrene P-1, the Will Corporation “Diaphane” and “Green Diaphane”, and the du Pont “Lucite” methyl methacrylate polymer were examined, and the possibility of use of some other plastics was also explored. The first 5 mentioned were tested for color preservation of a variety of stains in comparison with Canada balsam and Clarite X. From this point of view polystyrene, the Hartman Leddon “H.S.R.” and the Fisher “Permount” resins were the most satisfactory, then the “Diaphanes”. Both “Permount” and “H.S.R.” show some yellowing. The H.S.R. with a melting point of 115°C, the Permount with 150°C. melting point, and the Polystyrene with a thermal denaturation point above 220°C. all excell Canada balsam in heat resistance. Trimethylbenzene, cymene and monoamylbenzene appear to be the best solvents for polystyrene. Mounts made in a solution of 20 g. polystyrene in 100 ml. trimethylbenzene can be packed flat slide to slide in 24 hours after mounting without sticking together.

This report is not intended to deprecate the use of other resinous mounting media which have not as yet been tested or compared with those mentioned herein.     

Neurons as sensors: individual and cascaded chemical sensing

A single neuron sensor has been developed based on the interaction of gradient electric fields and the cell membrane. Single neurons are rapidly positioned over individual microelectrodes using positive dielectrophoretic traps. This enables the continuous extracellular electrophysiological measurements from individual neurons. The sensor developed using this technique provides the first experimental method for determining single cell sensitivity; the speed of response and the associated physiological changes to a broad spectrum of chemical agents. Binding of specific chemical agents to a specific combination of receptors induces changes to the extracellular membrane potential of a single neuron, which can be translated into unique “signature patterns” (SP), which function as identification tags. Signature patterns are derived using Fast Fourier Transformation (FFT) analysis and Wavelet Transformation (WT) analysis of the modified extracellular action potential. The validity and the sensitivity of the system are demonstrated for a variety of chemical agents ranging from behavior altering chemicals (ethanol), environmentally hazardous agents (hydrogen peroxide, EDTA) to physiologically harmful agents (pyrethroids) at pico- and femto-molar concentrations. The ability of a single neuron to selectively identify specific chemical agents when injected in a serial manner is demonstrated in “cascaded sensing”.     

A comparison of eating habits between retired or semi-retired aged subjects and younger subjects in full-time work

An analysis of eating habits in older retired subjects (“No Work group”) and younger subjects employed in full-time work (“Work group”) has been carried out. It used a questionnaire that assessed why individuals chose to eat or not to eat meals during the course of the day, and subjective responses to the meals. The questionnaire was answered every three hours over a “typical week” which, for the Work group, entailed working during the weekdays and resting at the weekend. For the “No Work” group, breakfast was the most frequently taken meal of the day whereas, for the “Work” group, this meal was often missed. Patterns of meal intake were not significantly different between the weekdays and weekend for the “No Work” group, but the “Work” group ate more hot food at the weekend. The reasons cited for eating/not eating a meal and for choosing the type of meal eaten were dominated by hunger/lack of hunger in both groups. In addition, whereas habits were also important for the “No Work” group, it was time availability or the lack of it that was of major importance to the Work group, though this was significantly less important at the weekend. Meals which required more time for preparation and cooking were appreciated significantly more (appetite before the meal, enjoyment during it, and satiety afterwards) than meals such as snacks and cold food, which could be prepared more quickly. Some implications of these results, with regard to regular meals acting as a social zeitgeber in older subjects and the additional constraints imposed upon night workers, are considered.     

The development of a “microtitre” fluctuation test for the detection of indirect mutagens, and its use in the evaluation of mixed enzyme induction of the liver

The “Microtitre” Fluctuation test recently introduced for the detection of direct mutagens has been adapted for the detection of indirect mutagens through the incorporation of an “S9-mix” metabolic system. It compares favourably with Greens' original method for the detection of a range of chemical mutagens.

The technique has been employed in the evaluation of mixed enzyme induction using phenobarbitone and β-naphthoflavone (benzoflavone). as a safe substitute for Aroclor-1254. The post-mitochondrial preparations from rats induced with the combined inducers had a similar “metabolic competence” to those derived from Aroclor induced animals. Such a combination would therefore provide a useful alternative to Aroclor-1254 for routine screening.

It was found that the level of “S9” present in the metabolic system greatly affected the quantitative mutagenic response. This varied considerably from chemical to chemical and underlined the need for such preliminary investigations in routine screening.     

The Lower Row Monkey Cage: An Overlooked Variable in Biomedical Research

A survey of 96 primatological articles revealed that cage location of research monkeys is rarely mentioned, although the environment of upper and lower row-housed animals markedly differs in terms of light quality, light intensity, and living dimension. Not accounting for these uncontrolled variables may increase variability of data and, consequently, the number of experimental animals needed to obtain statistically acceptable results. This study concluded that single-tier housing would be an important refinement of research methodology. Such housing would (a) enable all animals of a room to use the “arboreal ”dimension of their enclosure and retreat to “safe ”vantage points above the human “predator, ”(b) offer all animals access to uniform light, and (c) provide more favorable conditions for professional animal care.     

Contribution of response surface design to the development of glycerolysis systems catalyzed by commercial immobilized lipases

Two commercial immobilized lipases (“Lipozyme® IM” and “Novozym® 435”) were tested as biocatalysts for the glycerolysis of olive residue oil in n-hexane aimed at the production of monoglycerides (MG) and diglycerides (DG). A central composite rotatable design (CCRD) was followed to model and optimize glycerolysis as a function of both the amount of biocatalyst (L) and of the molar ratio glycerol/triglycerides (Gly/TG). For both biocatalysts, the production of free fatty acids (FFA) was described by second order models. In terms of MG and DG production, as well as of TG conversion, the best fits were obtained with first-order models. The highest MG productions were in the range 43–45% (w/w, on the basis of total fat) for both biocatalysts tested at a (Gly/TG) ratio of one. In the case of “Novozym 435”, the lowest load used (12%, w/w) gave the best results, in contrast with “Lipozyme IM” with which a concentration of about 26% (w/w) was necessary to obtain the highest production. Under these conditions, the amount of FFA produced was about 2% and 10% (w/w), respectively, for “Novozym 435” and “Lipozyme IM” catalyzed systems. Considering both FFA production and lipase loading, “Novozym 435” was shown to be a better biocatalyst for the glycerolysis of olive residue oil in n-hexane, aimed at the production of MG, than “Lipozyme IM”.     

Subdivision of the G1 phase of human glia cells in culture

Human glia cells blocked post-mitotically by serum deprivation require about 8–12 h of continuous stimulation by growth factors to become committed to DNA synthesis. DNA synthesis begins about 5 h after growth factor withdrawal. The length of time until the S phase began and the length of the apparent commitment period, i.e. the time when cells progressed towards the G1/S transition point even in the absence of growth factors were independent of the nature of the growth factors studied (calf serum, platelet-rich human serum, epidermal growth factor). Epidermal growth factor and calf serum were mutually interchangeable during the pre-commitment period. Increasing cell density reduced the number of cells which entered DNA synthesis, but had no effect on the length of the apparent commitment period or the latent time until DNA synthesis commenced. The requirement for a long exposure to a growth factor may be an important safeguard in normal cells against “accidental” entry into the cell cycle, since malignant glia cells do not show the same requirement.     

DNA interaction with biologically active divalent metal ions: binding constants calculation

In our previous work we have shown that under the action of Cu²⁺, Mn²⁺ and Ca²⁺ ions DNA is able to transit into a compact state in aqueous solution. In the present work we carried out calculations of binding constants for divalent metal ions interacting with DNA in terms of the macromolecule statistical sum. The formula for calculation of the binding constants and cooperativity parameters was proposed. It was shown that on the “coil state”–“compact (globule) state” transition a single DNA molecule may undergo the first-order phase transition while the transition of the assembly of average DNA chains is of sigmoidal character typical of the cooperative and continuous transition.