Alternative reproductive modes of Atlantic forest frogs

Diversity in reproductive modes is well known in amphibians, mainly among anurans, which are characterized by a diversity in breeding biology that exceeds that of any other tetrapod. Currently, 39 reproductive modes are recognized among anurans and some species display more than one mode. The breeding biology of some Brazilian Atlantic forest anurans was investigated for this study. We observed unreported reproductive modes for six species, variability in the reproductive modes of individuals of the same species (whereby some individuals of a given population displayed unusual reproductive modes when the physical conditions of the breeding site were suboptimal), and variations within the modes. These observations suggest possible evolutionary steps for the reproductive modes. Anuran breeding biology seems to be more diverse than previously reported, and a character matrix could be constructed to describe the total range of variation of the anuran reproductive modes.     

RF absorption involving biological macromolecules

The fundamental intramolecular frequency of a globular protein can be obtained from the measurements of acoustic velocities of bulk protein matter. This lowest frequency for common size molecules is shown to be above several hundred GHz. All modes below this frequency would then be intermolecular modes or bulk modes of the molecule and surrounding matter or tissue. The lowest frequency modes of an extended DNA double helix are also shown to be bulk modes because of interaction with water. Only DNA modes, whose frequency is well above 4 GHz, can be intrahelical modes, that is, confined to the helix rather than in the helix plus surroundings. Near 4 GHz, they are heavily damped and, therefore, not able to resonantly absorb. Modes that absorb radio frequency (RF) below this frequency are bulk modes of the supporting matter. Bulk modes rapidly thermalize all absorbed energy. The implication of these findings for the possibility of athermal RF effects is considered. The applicability of these findings for other biological molecules is discussed.     

The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies

The metabolism of a cell can be viewed as a weighted sum of elementary modes. Due to the multiplicity of modes the identification of the individual weights represents a non-trivial problem. To enable the determination of weighting factors we have identified and implemented two gene deletions in combination with defined growth conditions that limit the metabolism from 4374 original elementary modes to 24 elementary modes for a non-PHB synthesizing control and 40 modes for a PHB synthesizing strain. These remaining modes can be further grouped into five families that have the same overall stoichiometry. Thus, the complexity of the problem is significantly reduced, and weighting factors for each family of modes could be determined from the measurement of accumulation rates of metabolites. Moreover, it is shown that individual weights are inversely correlated with the entropy generated by the operation of the used pathways defined in elementary modes. This suggests that evolution developed cellular regulatory patterns that permit diversity of pathways while favoring efficient pathways with low entropy generation. Furthermore, such correlation provides a rational way of estimating metabolic fluxes based on the thermodynamic properties of elementary modes. This is demonstrated with an example in which experimentally determined, intracellular fluxes are shown to be highly correlated with fluxes computed based on elementary modes and reaction entropies. The analysis suggests that the set of elementary modes can be interpreted analogous to a metabolic ensemble of quantum states of a macroscopic system.     

Evolution of Protein Binding Modes in Homooligomers

The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of protein binding modes from nine families of homooligomers and mapped 60 different binding modes and oligomerization states onto the phylogenetic trees of these families. We observed a significant tendency for the same binding modes to be clustered together and conserved within clades on phylogenetic trees; this trend is especially pronounced for close homologs with 70% sequence identity or higher. Some binding modes are conserved among very distant homologs, pointing to their ancient evolutionary origin, while others are very specific for a certain phylogenetic group. Moreover, we found that the most ancient binding modes have a tendency to involve symmetrical (isologous) homodimer binding arrangements with larger interfaces, while recently evolved binding modes more often exhibit asymmetrical arrangements and smaller interfaces.     

Humidity levels drive reproductive modes and phylogenetic diversity of amphibians in the Brazilian Atlantic Forest

Aim The diversity of reproductive modes among amphibians constitutes a striking example of how differences in the biology of species provide important explanations for species distribution patterns on a broad scale. We hypothesize that sites with a higher humidity level will support more modes of reproduction than drier sites and will consequently exhibit a higher phylogenetic diversity. Furthermore, if there is a gradient in the tolerance of reproductive modes to desiccation, there will be a nested pattern in the composition of reproductive modes among sites. Location Twenty‐seven forest sites in the Brazilian Atlantic Forest. Methods Through a path analysis approach, we evaluated the direct and indirect effects of the humidity level on the number of reproductive modes, as well as the relative importance of both variables on amphibian phylogenetic diversity. A nestedness analysis was used to quantify the extent to which the compositions of both species and reproductive modes in drier sites correspond to subsets of those in sites with higher annual precipitation. Results We found that the reproductive modes present in drier sites are non‐random subsets of those present in sites with higher humidity levels. Because reproductive modes are phylogenetically conserved among amphibians, sites with a greater number of reproductive modes supported greater phylogenetic diversity. Sites with high precipitation throughout the year provided suitable environmental conditions for a larger number of reproductive modes, whereas sites with low precipitation and typical seasonal climates supported only those reproductive modes specialized to resist desiccation. Main conclusions Our results show that humidity‐related variables are key environmental factors related to both the richness of reproductive modes and phylogenetic diversity. Our results support the hypothesis that the higher phylogenetic diversity found in moister sites reflects differences in the tolerance to desiccation among different reproductive modes. Given that reproductive modes are associated with susceptibility to desiccation, their incorporation into explanatory models may trigger a significant advance in the understanding of the mechanisms regulating the species richness and composition of amphibian communities.     

Large‐scale comparison of protein essential dynamics from molecular dynamics simulations and coarse‐grained normal mode analyses

A large‐scale comparison of essential dynamics (ED) modes from molecular dynamic simulations and normal modes from coarse‐grained normal mode methods (CGNM) was performed on a dataset of 335 proteins. As CGNM methods, the elastic network model (ENM) and the rigid cluster normal mode analysis (RCNMA) were used. Low‐frequency normal modes from ENM correlate very well with ED modes in terms of directions of motions and relative amplitudes of motions. Notably, a similar performance was found if normal modes from RCNMA were used, despite a higher level of coarse graining. On average, the space spanned by the first quarter of ENM modes describes 84% of the space spanned by the five ED modes. Furthermore, no prominent differences for ED and CGNM modes among different protein structure classes (CATH classification) were found. This demonstrates the general potential of CGNM approaches for describing intrinsic motions of proteins with little computational cost. For selected cases, CGNM modes were found to be more robust among proteins that have the same topology or are of the same homologous superfamily than ED modes. In view of recent evidence regarding evolutionary conservation of vibrational dynamics, this suggests that ED modes, in some cases, might not be representative of the underlying dynamics that are characteristic of a whole family, probably due to insufficient sampling of some of the family members by MD. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Higher Order Plasmonic Modes Excited in Ag Triangular Nanoplates by an Electron Beam

Ag triangular nanoplates are known to generate strong plasmonic resonances when excited by both light and electron beams. Experimental electron energy-loss spectra (EELS) and maps were acquired using an aberration-corrected JEOL-ARM microscope. The corner, edge and centre modes that are often observed in such structures were also observed in these measurements. In addition, novel higher order internal modes were observed and were found to be well reproduced by theoretical calculations using boundary element method (BEM). These modes are “dark modes” so are not observed in the optical extinction spectra. They are confined surface propagating modes and are analogous to laser cavity modes.     

Non-interacting modes for stress, strain and energy in anisotropic hard tissue.

The six non-interacting modes for stress, strain and energy in an orthotropic elastic model of human femoral cortical bone tissue are discussed and illustrated. The stress and strain modes are illustrated using the representation of the stress and strain fields around a circular hole in a flat plate of cortical bone subjected to a uniaxial field of tension as the example. The six modes play a role in the stress analysis of orthotropic elastic materials similar to the roles played by the hydrostatic and deviatoric non-interacting stress, strain and energy modes in isotropic elasticity. The biomechanical significance of the six non-interacting modes for stress, strain and energy in hard tissue is both practical and suggestive. The modes suggest a practical scheme for the representation of stress and strain fields in hard tissue. The existence of the modes suggests physical insights, for example, possible failure mechanisms or adaptation strategies possessed by the hard tissues.     

大肠杆菌编码区碱基片段的分析研究

对大肠杆菌1231个编码开始区域和1307个编码终止区域内的6碱基片段、4碱基片段和3碱基片段进行了统计,发现绝大多数4碱基和3碱基模式出现在盯对频率小于2的范围之内;在这两个区域中,出现最多的碱基片段是多聚A;编码开始区域和编码终止区域的碱基构成模式有明显区别;编码开始区域里GGA类的稀有片段恰恰是SD区域最偏好的碱基片段;以TAG或CTA构造的3碱基模式为编码开始区和编码终止区的禁用模式。     

In-Plane Plasmonic Modes in a Quasicrystalline Array of Metal Nanoparticles

We investigated the plasmonic modes in a two-dimensional quasicrystalline array of metal nanoparticles. The polarization of the modes is in the array plane. A simplified eigen-decomposition method is presented with the help of rotational symmetry. Two kinds of anti-phase ring modes with radial and tangential polarizations are of highest spatial localizations among all of plasmonic modes. For the leaky characteristic of the anti-phase ring modes, the highest fidelity mode in the quasicrystalline array is found to be tangential polarized mode, whereas normal-to-plane polarized mode in the circular ring. The leaky characteristics and spatial localizations of other plasmonic modes are also studied, for example, collective vortex mode that may be a candidate to form negative responses in plasmonic device and collective radial mode that may be used to generate light sources with radial polarizations.     

Plasmonic Modes of Ag Nanoshell Excited by Bi-Dipole

We studied plasmonic dipole, quadrupole, and sextupole modes of Ag nanoshell (NS) excited by a pair of aligned radial electric dipoles (bi-dipole) in symmetric and antisymmetric configurations by using dyadic Green’s functions. The mutual excitation rate and the radiative and nonradiative powers of bi-dipole in the presence of Ag NS were analyzed. Our results show that these modes are in accordance with the surface plasmon resonances of Ag NS irradiated by a polarized plane wave. In addition, the mutual excitation rate retains local maxima at these modes. Moreover, the quadrupole and octupole modes are only excited in the cases of the symmetric radial bi-dipole, while the dipole and sextupole modes are only excited in the cases of the antisymmetric ones. The dipole mode is broadband, while the other higher-order modes are narrowband. Moreover, all of these plasmonic modes are red-shifted as the ratio of the core radius to the shell thickness increases.     

Raman and infrared studies of nucleosides at high pressures: I. Adenosine.

Room temperature Raman and infrared (IR) spectra of crystalline adenosine at pressures between 1 atm and 10 GPa are reported. Vibrational modes were identified through assignments in the literature. Many modes were found to increase in frequency with pressure; however, some irregularities were observed. Discontinuities were observed in numerous Raman and IR modes near 2.5 GPa, indicating a phase transition. The modes associated with the glycosidic bond shift significantly down in frequency near this pressure, suggesting a weakening of the associated bond. The IR modes associated with hydrogen-stretching motions were found to decrease in frequency with pressure.     

Stability of hybrid modes of a single-component electron plasma containing an admixture of background gas ions

The spectrum of eigenmodes of a waveguide completely filled with a cold electron plasma containing a small admixture of ions produced due to electron-impact ionization of background gas atoms is calculated numerically. The calculations were performed within the entire range of allowable values of the radial electric and longitudinal magnetic fields for both magnetized and unmagnetized ions by using the earlier derived nonlocal dispersion relation [Plasma Phys. Rep. 36, 563 (2010)]. The spectrum consists of three families of electron modes with frequencies equal to the Doppler-shifted upper and lower hybrid frequencies and modified ion cyclotron (MIC) modes. When the Doppler shift caused by electron rotation in the crossed electric and magnetic fields compensates for the hybrid frequency, the electron modes become low-frequency modes and interact with the ion modes. For m = 1, only the lower hybrid modes can be low-frequency ones, whereas at m ≥ 2, both lower and upper hybrid modes can be low-frequency ones. The spectrum of modes having the azimuthal number m = 2 is thoroughly analyzed. It is shown that, in this case, the lower hybrid modes behave similar to the m = 1 modes. The dispersion curves of the upper hybrid modes intersect with all harmonics of the MIC frequency (positive, negative, and zero) and are unstable in the vicinities of the intersections. The maximum value of the instability growth rate is several times higher than the ion plasma frequency. The MIC modes are unstable within a wide range of the field strengths, and their growth rates are two orders of magnitude slower. Instabilities are caused by the relative motion of electrons and ions (the transverse current) and the anisotropy of the ion distribution function.     

Coupled transverse modes of coaxial metal waveguides completely filled with magnetoactive current-carrying plasma

The propagation of ordinary bulk modes coupled with extraordinary surface modes in coaxial metal waveguides completely filled with cold magnetoactive plasma is investigated theoretically. The interaction between modes propagating across the waveguide axis in the presence of the axial and azimuthal components of the external magnetic field is examined. The effect of the azimuthal magnetic field on the dispersion properties of these modes is thoroughly studied for the case of a uniform plasma.     

Intermediate and stable redox states of cytochrome c studied by low temperature resonance Raman spectroscopy

Stabilized intermediate redox states of cytochrome c are generated by radiolytic reduction of initially oxidized enzyme in glass matrices at liquid nitrogen temperature. In the intermediate states the heme group is reduced by hydrated electrons, whereas the protein conformation is restrained close to its oxidized form by the low-temperature glass matrix. The intermediate and stable redox states of cytochrome c at neutral and alkaline pH are studied by low-temperature resonance Raman spectroscopy using excitations in resonance with the B (Soret) and Q1 (beta) optical transitions. The assignments of the cytochrome c resonance Raman bands are discussed. The observed spectral characteristics of the intermediate states as well as of the alkaline transition in the oxidized state are interpreted in terms of oxidation-state marker modes, spin-state marker modes, heme iron--axial ligand stretching modes, totally symmetric in-plane porphyrin modes, nontotally symmetric in-plane modes, and out-of-plane modes.     

Flux modules in metabolic networks

The huge number of elementary flux modes in genome-scale metabolic networks makes analysis based on elementary flux modes intrinsically difficult. However, it has been shown that the elementary flux modes with optimal yield often contain highly redundant information. The set of optimal-yield elementary flux modes can be compressed using modules. Up to now, this compression was only possible by first enumerating the whole set of all optimal-yield elementary flux modes. We present a direct method for computing modules of the thermodynamically constrained optimal flux space of a metabolic network. This method can be used to decompose the set of optimal-yield elementary flux modes in a modular way and to speed up their computation. In addition, it provides a new form of coupling information that is not obtained by classical flux coupling analysis. We illustrate our approach on a set of model organisms.     

Raman and Infrared Studies of Nucleosides at High Pressures: I. Adenosine

Abstract

Room temperature Raman and infrared (IR) spectra of crystalline adenosine at pressures between 1 atm and 10 GPa are reported. Vibrational modes were identified through assignments in the literature. Many modes were found to increase in frequency with pressure; however, some irregularities were observed. Discontinuities were observed in numerous Raman and IR modes near 2.5 GPa, indicating a phase transition. The modes associated with the glycosidic bond shift significantly down in frequency near this pressure, suggesting a weakening of the associated bond. The IR modes associated with hydrogen-stretching motions were found to decrease in frequency with pressure.     

Elementary mode analysis to study the preculturing effect on the metabolic state of Lactobacillus rhamnosus during growth on mixed substrates

Quantification of metabolism through elementary modes offers insights into the working of a metabolic network. We have determined the fluxes of elementary modes through linear optimization using the stoichiometry of the elementary modes as a constraint. We apply this methodology to obtain insights into the effect of preculturing on growth of Lactobacillus rhamnosus on medium containing mixed substrates. L. rhamnosus, a microaerophilic organism, produces flavor compounds such as diacetyl and acetoin during growth on glucose and citrate. The uptake of citrate has been shown to be sensitive to preculturing states of the cells. Elementary modes demonstrated that citrate was utilized by the organism as a sole carbon source. Further, both glucose and citrate was catabolized by this organism through aerobic and anaerobic routes. The flux analysis indicated that only 21 elementary modes were operational during growth of L. rhamnosus on glucose and citrate. Glucose specifically accounted for 6 elementary modes, while the remaining 15 involved citrate as substrate. The modes associated with glucose were mainly operational when cells were precultured on glucose. It was observed that all the 21 modes contributed to the fluxes when the cells were precultured on citrate. The NADH recycling through lactate formation and oxygen uptake were dependent on the preculturing state. The analysis also demonstrated that preculturing on citrate yielded better productivity of diacetyl and acetoin.     

Description of base motion and role of excitations in the melting of poly(dG).poly(dC).

We study the contribution of various vibrational modes to the melting of poly(dG).poly(dC). We find that the principal contribution comes from the H-bond breathing modes that have been observed in Raman scattering and that we have associated with helix melting. We show the softening of these modes on approach to melting in agreement with the observed behavior. We also describe the contribution to melting from base rotation modes that others have suggested are important in melting.