The measurement process in biological systems: a new phenomenology.

A quantum theoretic approach to the problem of specific biological interactions at the molecular level, is presented. The concept of a “measuring system” in analogy with the enzyme macromolecule is used. The main hypothesis is that in the course of an enzymic reaction, the enzyme will specify the eigenvalues of the observables associated with the substrate, on some particular quantum states. Then, any “perturbation” induced in the substrate, will also be specified by the enzyme. In this context, the enzymic substrate is “perturbed” by an electromagnetic field and the physical transition S → S¹ thus induced is “measured” in the E_(S) + S¹ enzyme reaction, as compared with the control E_(S) + S reaction. The effect on the enzyme reaction is manifested by an enhancement of the reaction rate appearing periodically at well defined substrate irradiation times. The minimum substrate irradiation time inducing the first effect, termed t_m and the fixed time period that always appears to delimit two successive rate effects, termed the τ-parameter, are enzyme dependent. The same idea was used to devise an experimental model for the study of some more general interactions, within cellular systems. The growth of auxotrophic micro-organisms in minimal media supplemented with irradiated growth factors was followed. The pattern of growth stimulations obtained with this model, displays a similarity with the periodic enhancements of enzymic rates, obtained with irradiated substrates. This new type of evidence may suggest a characteristic of biological specificity, previously unrecognized.     

On a new symmetry in biological systems

A new physical property, called resonance of the B-type is hypothetically attached to the λ =546 nm irradiated crystalline (small) molecules. In this respect an up or down configuration is assumed for those states obtained through irradiation times that are multiples of 5 sec. With these assumptions, the cellular receptors that may detect these states appear to belong to three classes: the up, down and alternatively mixed up-down. Using the classic formalism of eigenvectors and eigenvalues, a simple spectroscopic type of formula is derived, through which all the possible states of the above characteristic may be obtained.     

QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity

Recent technological advances have enabled the generation of large amounts of data consisting of RNA sequences and their functional activity. Here, we propose a method for extracting secondary structure features that affect the functional activity of RNA from sequence–activity data. Given pairs of RNA sequences and their corresponding bioactivity values, our method calculates position-specific structural features of the input RNA sequences, considering every possible secondary structure of each RNA. A Ridge regression model is trained using the structural features as feature vectors and the bioactivity values as response variables. Optimized model parameters indicate how secondary structure features affect bioactivity. We used our method to extract intramolecular structural features of bacterial translation initiation sites and self-cleaving ribozymes, and the intermolecular features between rRNAs and Shine–Dalgarno sequences and between U1 RNAs and splicing sites. We not only identified known structural features but also revealed more detailed insights into structure–activity relationships than previously reported. Importantly, the datasets we analyzed here were obtained from different experimental systems and differed in size, sequence length and similarity, and number of RNA molecules involved, demonstrating that our method is applicable to various types of data consisting of RNA sequences and bioactivity values.     

Ligand-receptor interactions: a new method for determining the binding parameters

A new experimental procedure and new plot coordinates that allow determination of the binding parameters of ligand-acceptor interaction have been proposed. Instead of titration of a constant concentration of receptors with changing concentrations of ligand, as requested by the well-known methods of Klotz and Scatchard, a series of sequential dilutions of the reacting ligand-receptor mixture is suggested. This allows the application of a new coordinate system that transforms the binding isotherms into straight lines. The case of one acceptor with two classes of receptors with different binding constants is also considered briefly, where the correspondent graphs are nonlinear. It is suggested that in some cases this approach can be a simple and convenient substitute of the broadly used methods of Klotz and Scatchard.     

Microbial Resource Management revisited: successful parameters and new concepts

In the twenty-first century, scientists will want to steer the microbial black box in (engineered) ecosystems, rather than only study and describe them. This strategy led to a new way of thinking: Microbial Resource Management (MRM). For the last few years, MRM has been utilized to consolidate and communicate our acquired knowledge of the microbiome to many areas of the scientific community. This shared knowledge has brought us closer to formulating a plan toward the analysis, and at a later stage, the management of our varied microbial communities and to look at ways of harnessing their unique abilities for future practices. We require this acquired knowledge for a more sustainable solution to our ongoing global challenges such as our diminishing energy and water supply. Like any successful concept, MRM must be updated to adapt to new molecular technologies, and thus, in this review, MRM has been reengineered to encompass these changes. This review reports how MRM has been used successfully over the last few years within various environments and how we can broaden its capabilities to increase its compliance in the face of state of the art ever changing technologies. Not only have we reengineered and improved MRM, but also we have discussed how newly formed relationships between technologies can provide the full picture of these complex microbial communities and their interactions for future opportunities.     

An efficient method for extracting plasma ions in laser isotope separation systems

The possibility of using a Hall-current accelerator to extract ions from a partially ionized plasma produced by selective laser isotope photoionization of atomic vapor is examined. A mechanism for ion acceleration is investigated using one-dimensional time-dependent equations of two-fluid magnetohydrodynamics. The current cutoff due to the ion space charge is prevented by electron emission. It is shown that, at an accelerating voltage of 25–50 V and emission current density of several mA/cm², the ion component is accelerated throughout the entire plasma volume up to a velocity of ～10⁵ cm/s in a few microseconds. The influence of resonant charge exchange and secondary ionization by electrons on both the acceleration dynamics and selectivity degradation is taken into account. It is shown that the Hall-current extractor allows one to avoid selectivity degradation even when the plasma size exceeds the charge-exchange mean free path by one order of magnitude.     

Green light effects on biological systems: a new biophysical phenomenon

This paper reports a new phenomenon connected with the influence of green light (GL) on biological systems. Our experiments have revealed an antioxidant effect of GL on cells subjected to lethal doses of UV at the cellular level and a protective effect of GL on DNA denatured by UV, coupled with a structural modification of DNA macromolecules under GL irradiation, at the molecular level. Mouse melanocyte cultures are subjected to UV irradiations with L₅₀ fluxes of 16.0 J m^− 2 s^− 1. GL is obtained from a strontium aluminate pigment, which emits GL under UV activation. Cells grown in GL, prior to UV irradiation, present a clear surprising protective effect with surviving values close to the controls. A GL antioxidant effect is suggested to be mediated through GL influence on cellular water cluster dynamics. To test this hypothesis, reactive oxygen species (ROS) are determined in cell cultures. The results revealed a decrease of cellular ROS generation in the UV-irradiated samples protected by a previous 24 h of GL irradiation. At the DNA level, the same type of GL protection against UV damage is recorded by gel electrophoresis and by UV spectroscopy of the irradiated DNA molecules. Two physical methods, impedance spectroscopy and chronoamperometry, have revealed at the level of GL-irradiated DNA molecules spectral modifications that correlate with the UV spectroscopy results. The interaction between the chargeless photons and the field of water molecules from the cellular compartments is discussed in relation with the new field of macroscopic quantum coherence phenomena.     

Carotenoid research: History and new perspectives for chemistry in biological systems

The history of carotenoid research as this progressed from chemistry to biochemistry and biology is outlined. Proposed roles of carotenoids in eye health, as antioxidants, and in protection against cancer and other degenerative diseases, as well as stimulatory effects on the immune system and metabolism are covered. Proposed biological actions must be consistent with the chemistry of carotenoids in the largely aqueous biological systems, which may differ from the known chemistry of carotenoids in organic solvents. In particular, carotenoids tend to form aggregates. The effects of this aggregation and of other molecular interactions in vivo are likely to be crucial to biological activity. These perspectives of the chemistry of carotenoids and carotenoid free radicals are examined and the need for carotenoid samples used in experimental work to be pure and free from breakdown products and pro-oxidant peroxides is emphasised.This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.     

A spectrophotometric method for estimating hemin in biological systems

Hemin chlorides exhibit two absorption maxima in the Soret region, one at about 360-380 nm (S' band) and the other between 400 and 430 nm (S band). We present here a simple and fast spectrophotometric assay to determine concentration of hemin between 1.15 and 9.20 microM employing the Soret region (S' band) as a reference. In this method the hemin is quantitatively extracted from biological materials by acidified chloroform. By recording the absorbance of the chloroform extract at its maximum peak at 388, 450, and 330 nm and applying the correction formula A(c)=2A388-(A450+A330), a very good linear correlation between the A(c) and the concentration of hemin is attained. The method can be used to estimate hemin in the presence of protein (0.06-5.00 mg/ml) and porphyrin (0.19-2.97 microM). Compared with the pyridine hemochromogen method, the assay reported here is highly reproducible, with 15- to 30-fold more sensitivity, and it allows the quantification of four times lower hemin concentrations.     

Photochrome-labeling method in study of dynamics of biological systems.

The theoretical considerations and experimental evidences discussed in this paper indicate that quantitative study of photochromic processes in labeled objects open up new possibilities for investigating microviscosity and conformation transitions in biological systems. The proposed method of photochrome labeling features higher sensitivity and simplicity, and uses labels which are more stable under physiological conditions compared with traditional spin labels.     

Peptide-mediated interactions in biological systems: new discoveries and applications

Peptide-mediated interactions play very important roles in cellular processes. Recent years have seen much activity in the discovery of new bioactive peptides, and interactions mediated by protein-peptide binding events. At the same time, computational approaches continue to be developed that allow protein-peptide interactions to be discovered with great accuracy. There are also a growing number of chemicals that can target these interactions with various applications in disease. Both new discoveries and predictions suggest that these protein-peptide interactions play greater roles in cellular processes than previously thought. We propose that projects to uncover the protein-peptide repertoire used in Nature in a systematic way will have numerous applications in molecular biology and medicine.     

A method for the detection of superoxide in biological systems

The ability to detect superoxide in biological milieu is filled with a number of difficult problems. For example, the ferricytochrome c assay method cannot be used in the presence of NADPH-cytochrome P-450 reductase since cytochrome c is preferentially reduced by this enzyme. We have found that the superoxide-dependent oxidation of one particular hydroxylamine, 2-ethyl-1-hydroxy-2,5,5-trimethyl-3-oxazolidine, to its corresponding nitroxide, 2-ethyl-2,5,5-trimethyl-3-oxazolidinoxyl, can be used to quantitate superoxide production by hepatic microsomes and purified enzymes. We determined that this assay method is free from most of the problems inherent in other methods for the identification of superoxide.     

Phosphorus-31 two-dimensional solid-state exchange NMR. Application to model membrane and biological systems.

Two-dimensional solid-state 31P NMR has been used to investigate the orientational exchange of phospholipids in gel and liquid-crystalline aqueous multilamellar dispersions and oriented multibilayers, and in biological membranes. In liquid-crystalline L alpha multilamellar dispersions, orientational exchange originates from the lateral diffusion of phospholipid molecules over the curved surface of the liposomes and is manifest by an increase in off-diagonal intensity, which correlates the 90 and 0 degrees orientations of the membrane normal with respect to the magnetic field when the system is fully exchanged. Spectral simulations of the time evolution of exchange allowed determination of the correlation times tau d for lateral diffusion. For DMPC and DPPC at comparable reduced temperatures, tau d values of 44 and 8 ms were obtained, respectively. The nature and rate of exchange observed for POPE at 30 degrees C is similar to that of DMPC at the same temperature. The measured correlation times are consistent with diffusion rates obtained by FRAP for liposomes with radii in the 1 micron range. In the gel phase of DPPC (30 degrees C), little orientational exchange is observed at mixing times up to 200 ms, demonstrating that the lateral diffusion is very slow. The correlation time for orientational exchange obtained from spectral simulations was approximately 900 ms; thus, exchange in the gel state is at least two orders of magnitude slower than in the liquid-crystalline state. In the P beta (ripple) phase, at temperatures between 34 and 39 degrees C, significant exchange is observed for mixing times between 50 and 200 ms. Exchange is also observed in oriented samples of DPPC in the P beta phase for mixing times of 50 ms, but not for oriented liquid-crystalline samples for mixing times up to 100 ms. The exchange observed in the ripple phase could originate from rapid lateral diffusion of "fast" diffusing phospholipid within defect structures, and/or from "slow" lateral diffusion of ordered phospholipid over the ripples. 2D experiments were also performed on pig erythrocyte ghosts and on intact pig spinal cord. Significant orientational exchange was observed with the erythrocyte ghosts at a mixing time of 200 ms, but almost no exchange was observed with the spinal cord at the same mixing time. Spectral simulations suggest tau d values of approximately 400 ms and 1.3 s for the erythrocyte ghosts and spinal cord at 30 degrees C.(ABSTRACT TRUNCATED AT 400 WORDS)