Extending the range of FRET—the Monte Carlo study of the antenna effect

The problem of extending the utilizable range of Förster resonance energy transfer (FRET) is of great current interest, due to the demand of conformation studies of larger biological structures at distances exceeding typical limiting distance of 100 Å. One of the ways to address this issue is the use of so-called antenna effect. In the present work, the influence of the antenna effect on the FRET efficiency is investigated by the Monte Carlo analysis. The previously published results Bojarski et al. (J Phys Chem B 115:10120–10125, 2011) indicate that using a simple model of donor linked with a protein labeled with multiple acceptors, significantly increases the transfer efficiency in comparison with donor–single acceptor system. The effect is stronger if the transition moments of acceptors are mutually parallel. In this work, to extend the scope of possible biological systems to be analyzed, different distributions of donor–acceptors distance are analyzed, as well as the size and shape of the attached molecule.     

The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009 ; Meyer 2011 ; Nosil 2012 ). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009 ), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009 ), or pollinator‐mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012 ), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011 ). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006 ), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011 ). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. ( 2014 ) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early‐stage divergence in Midas cichlids.     

SAXS study of the snake toxin α-crotamine

-crotamine is a small toxic protein (42 amino acid residues with three disulphide bridges) present in the venom of Crotallus durissus terrificus. Molecular parameters (R _g=13.7 Å, S=3,000 Ų, V=9,200 ų and D _max=40 Å) were derived from SAXS curves obtained from a solution of this protein at pH=4.5. An excellent agreement between the experimental distance distribution curve and that calculated from a model consisting of two lobes linked by the Cys(18)-Cys(30) disulphide bridge.     

Determination of the number of degrees of freedom of the trapeziometacarpal joint–An in vitro study

ObjectiveMost of the studies about trapeziometacarpal joint assume that it exhibits only two independent degrees of freedom, but the experimental or theoretical support for considering a two-degrees of freedom model is not always clear.Materials and methodsTherefore, an in vitro kinematic study has been designed to demonstrate, from experimental data, that only two of the trapeziometacarpal degrees of freedom (i.e., flexion/extension and adduction/abduction) are non-null and independent. Several movements of maximal amplitude in flexion, abduction and circumduction have been realized and the relative position and orientation of the segment coordinate system embedded on the first metacarpal with respect to that embedded on the trapezium have been collected using electromagnetic sensors. The trapeziometacarpal rotations have been described using a joint coordinate system and the joint displacements have been evaluated on the axes of this coordinate system.ResultsThe root mean square (RMS) values of the joint displacement components have been found small enough to assume that the trapeziometacarpal joint has no translation degrees of freedom. A paraboloid coupling equation has been found between the internal/external rotation angle and the two other, flexion/extension and adduction/abduction, angles.ConclusionThus, this study demonstrates that the trapeziometacarpal joint has only two independent rotational degrees of freedom, and further, the described methodology could also be used to determine the coupling laws between degrees of freedom of various joints.     

Progress of a half century in the study of the Luria-Delbrück distribution

The Luria-Delbrück mutation model has been mathematically formulated in a number of ways. This review article examines four most important formulations, focusing on important practical issues closely linked with the distribution of the number of mutants. These issues include the probability generating functions, moments (cumulants), computational methods and asymptotics. This review emphasizes basic principles which not only help to unify existing results but also allow for a few useful extensions. In addition, the review offers a historical perspective and some new explanations of divergent moments.     

A study of the nature of the immediate precursor of the extracellular α-amylase of Bacillus amyloliquefaciens. A reappraisal

1. A defined medium was devised for use in washed-cell experiments with post-exponential-phase cultures of Bacillus amyloliquefaciens. The medium allowed alpha-amylase to be secreted, bacterial concentration to increase and l-[U-(14)C]valine to be incorporated into protein at a linear rate, which was the same as in a post-exponential-phase culture, for up to 6h. 2. Determination of the specific radioactivity of l-[U-(14)C]valine in the medium, the intracellular amino acid pool, the cellular protein and the isolated alpha-amylase, after a 3h incubation of washed cells in the defined medium, showed that at least 76% of the alpha-amylase secreted was synthesized de novo. 3. By isolating the alpha-amylase formed during a 6h incubation in the presence of l-[U-(14)C]valine it was shown that the specific radioactivity of the N-terminal valine, within the limits of experimental error, was the same as that of the total valine residues from the complete alpha-amylase molecule. 4. A consideration of these results in relation to the whole literature on the subject strongly supports the idea that there is no reason to suppose that extracellular alpha-amylase is formed from a high-molecular-weight precursor in B. amyloliquefaciens and closely related organisms with identical characteristics of exoenzyme secretion.     

Analysis of the musculoskeletal loading of the thumb during pipetting – A pilot study

Previous epidemiological studies indicate that the use of thumb-push mechanical pipettes is associated with musculoskeletal disorders (MSDs) in the hand. The goal of the current study was to analyze the loading in the muscle–tendon units in the thumb during pipetting. The hand is modeled as a multi-body linkage system and includes four fingers (index, long, ring, and little finger), a thumb, and a palm segment. Since the current study is focused on the thumb, the model includes only nine muscles attached to the thumb via tendons. The time-histories of joint angles and push force at the pipette plunger during pipetting were determined experimentally and used as model input; whereas forces in the muscle–tendon units in the thumb were calculated via an inverse dynamic approach combined with an optimization procedure. Results indicate that all nine muscles have force outputs during pipetting, and the maximal force was in the abductor pollicis brevis (APB). The ratio of the mean peak muscle force to the mean peak push force during the dispensing cycle was approximately 2.3, which is comparable to values observed in grasping tasks in the literature. The analysis method and results in the current study provide a mechanistic understanding of MSD risk factors associated with pipetting, and may be useful in guiding ergonomic designs for manual pipettes.     

Spectral study of the interaction of DNA with benzothiazolyl-benz-α-chromene

Absorption and luminescence excitation and emission spectra of newly synthesized 2-(4-methylphenylimino)-3-(2 -benzothiazolyl)benz-alpha-chromene (BCBT) have been studied in the presence of various DNA concentrations. BCBT is characterized by the existence of two different fluorescent systems, exhibiting radiationless fluorescence resonance energy transfer between them. In the range of molar ratios of polynucleotide/dye concentrations from 0 to 50, BCBT preferentially intercalates into DNA due to its benz-alpha-chromene fragment, whereas the 2-benzothiazolyl fragment is responsible for fluorescence.     

Is post-contrast MRI a valuable method for the study of the nutrition of the intervertebral disc?

Decreased nutrition has been proposed as a potential mechanism leading to intervertebral disc degeneration. A method to investigate it in vivo is the MRI evaluation of the transport of a paramagnetic contrast agent, which is assumed to diffuse through the endplate to the disc using the same mechanisms as the cell nutrients. However, previous numerical studies questioned the value of this method as a model to investigate disc nutrition. To assess its validity, a parametric osmoporoelastic finite element model of a lumbar intervertebral disc incorporating diffusion and convection of a solute (representing the contrast agent) was developed. A Taguchi sensitivity analysis was performed in order to assess the relevance of various parameters which influence the solute transport. Subsequently, a full-factorial sensitivity analysis was used to investigate specifically the diffusion coefficients of the contrast agent. The most important parameters in determining the results were the disc height, the diffusion coefficients and the pharmacokinetic of the contrast agent. However, diffusion coefficients values as measured in in vitro studies would lead to insubstantial enhancement of the MRI signal. Thus, transport mechanisms other than pure diffusion should be active in in vivo transport of the contrast agent. In conclusion, the study showed that post-contrast MRI may not be suited for a quantitative analysis, but only for a qualitative examination aimed for example to detect endplate lesions. Open questions remain on the use of post-contrast MRI for the investigation of the relevance of reduced nutrition as a trigger to disc degeneration.     

Advances in the study of protein–DNA interaction

Protein-DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper.     

Immunochemical study of transforming growth factor-β in the kidney of the rat and chicken

Transforming growth factor- (TGF-) is a homodimeric polypeptide of 25 kDa, which regulates cell growth and differentiation and influences extracellular matrix metabolism. Using immunochemical techniques, we identified TGF- in the loops of Henle and the collecting and Bellini ducts of rat kidney and in the loops of Henle of chicken kidney. Furthermore, we detected two TGF--immunoreactive proteins on kidney blots of the rat of 12.5 and 47 kDa, and three on chicken kidney blots of 12.5, 34, and 47 kDa. We suggest that the precursor forms of rat and chicken TGF-2 or 3, chicken TGF-4, and the mature form of all of them are expressed in the collecting and Bellini ducts of rat kidney and the loops of-Henle of rat and chicken kidney.     

Theoretical study of hydrogenation of the doubly aromatic B 7 − cluster

We have studied the influence of hydrogenation on the relative stability of the low-lying isomers of the anionic B₇⁻ cluster, computationally. It is known that the pure-boron B₇⁻ cluster has a doubly (σ- and π-) aromatic C_6v (³A₁) quasi-planar wheel-type triplet global minimum (structure 1), a low-lying σ-aromatic and π-antiaromatic quasi-planar singlet C_2v (¹A₁) isomer 2 (0.7 kcal mol⁻¹ above the global minimum), and a planar doubly (σ- and π-) antiaromatic C_2v (¹A₁) isomer 3 (7.8 kcal mol⁻¹ above the global minimum). However, upon hydrogenation, an inversion in the stability of the species occurs. The planar B₇H₂⁻ (C_2v, ¹A₁) isomer 4, originated from the addition of two hydrogen atoms to the doubly antiaromatic B₇⁻ isomer 3, becomes the global minimum structure. The second most stable B₇H₂⁻ isomer 5, originated from the quasi-planar triplet wheel isomer 1 of B₇⁻, was found to be 27 kcal mol⁻¹ higher in energy. The inversion in stability occurs due to the loss of the doubly aromatic character in the wheel-type global minimum isomer (C_6v, ³A₁) of B₇⁻ upon H₂−addition. In contrast, the planar isomer of B₇⁻ (C_2v, ¹A₁) gains aromatic character upon addition of two hydrogen atoms, which makes it more stable. Figure The B₇H₂-global minimum structure and its σ-aromatic and π-antiaromatic MOs Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

Mechanistic study of the structure–activity relationship for the free radical scavenging activity of baicalein

Density functional theory calculations were performed to evaluate the antioxidant activity of baicalein. The conformational behaviors of both the isolated and the aqueous-solvated species (simulated with the conductor-like polarizable continuum solvation model) were analyzed at the M052X/6-311 + G(d,p) level. The most stable tautomers of various forms of baicalein displayed three IHBs between O4 and OH5, O5 and OH6, and O6 and OH7. The most stable tautomer of the baicalein radical was obtained by dehydrogenating the hydroxyl at C6, while the most stable anion tautomer was obtained by deprotonating the C7 hydroxyl in gaseous and aqueous phases. The expected antioxidant activity of baicalein was explained by its ionization potentials (IPs) and homolytic O–H bond dissociation enthalpies (BDEs), which were obtained via the UM052X optimization level of the corresponding radical species. Heterolytic O–H bond cleavages (proton dissociation enthalpies, PDEs) were also computed. The calculated IP, BDE, and PDE values suggested that one-step H-atom transfer, rather than sequential proton loss–electron transfer or electron transfer–proton transfer, would be the most favorable mechanism for explaining the antioxidant activity of baicalein in the gas phase and in nonpolar solvents. In aqueous solution, the SPLET mechanism was more important.     

Does the antibacterial activity of silver nanoparticles depend on the shape of the nanoparticle? A study of the Gram-negative bacterium Escherichia coli

In this work we investigated the antibacterial properties of differently shaped silver nanoparticles against the gram-negative bacterium Escherichia coli, both in liquid systems and on agar plates. Energy-filtering transmission electron microscopy images revealed considerable changes in the cell membranes upon treatment, resulting in cell death. Truncated triangular silver nanoplates with a {111} lattice plane as the basal plane displayed the strongest biocidal action, compared with spherical and rod-shaped nanoparticles and with Ag(+) (in the form of AgNO(3)). It is proposed that nanoscale size and the presence of a {111} plane combine to promote this biocidal property. To our knowledge, this is the first comparative study on the bactericidal properties of silver nanoparticles of different shapes, and our results demonstrate that silver nanoparticles undergo a shape-dependent interaction with the gram-negative organism E. coli.     

A scanning electron-microscopic study of “supramarginal cells” in the pituitary cleft of the rat

Summary Unusual cells lying above the marginal cellular layer of the rat pituitary cleft were studied by SEM and TEM. These cells — from their location termed supramarginal cells — have a characteristically irregular cell body from which arise a number of long and thin branched processes ending among the microvilli and cilia of the marginal cells delimiting the anterior and posterior walls of the cleft. Some supramarginal cells are star-shaped elements with thin extensions, others have a triangular or spindle-shaped body from which emerge long ameboid processes with fibril-like projections. Miniblebs, miniruffles, occasional veils and short microvilli extend over the surface of these elements.Supramarginal cells are very similar to the Kolmer epiplexus cells originally found on the choroid plexus or other areas of the third ventricular wall where they are known as supraependymal cells.Present evidence suggests that supramarginal cells of pituitary cleft might have phagocytic properties and an hematogenous origin as monocytes and, as such, closely resemble Kolmer epiplexus cells of brain ventricles. Others might arise from folliculo-stellate cells or closely related marginal cells once they become free into the pituitary cleft.Supramarginal cells are recognized as motile phagocytes acting as scavengers and possibly regulating the extracellular environment of the cleft and associated adenohypophy-sial tissues. In considering the area where they are located supramarginal cells might assume a specific role in relation to the integrated neuroendocrine function of the hypothalamus-ventricle-hypophysial complex. To this complex the pituitary cleft is closely associated embryologically and anatomically.