Theory of the Anomalous Resonant Absorption of DNA at Microwave Frequencies−

Abstract

Aqueous solutions of oligopolymer DNA have been observed by Edwards, Davis, Swicord & Saffer to show structured absorption of microwave energy in the region of several gigahertz characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances. The inclusion of electromagnetic interactions with surrounding counter ions yields a richer space of possibilities for complex behavior of the combined system. A well defined resonant absorption peak appears when the molecular motion and the nearby solvent motion are even slightly decoupled. The microwave electric fields in the vicinity of the molecule provide a mechanism for such a decoupling not present for the case of electrically neutral solvent.     

Why structured water causes sharp absorption by DNA at microwave frequencies

Aqueous solutions of oligopolymer DNA have been observed by G.S. Edwards, C.C. Davis, M.L. Swicord and J.D. Saffer, Phys. Rev. Lett. 53, 1284 (1984) to show structured absorption of microwave energy in the region of several gigahertz, characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Although hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances, the molecular nature of the solvent in the near neighborhood of the polymer and- paradoxically- the strong water/polymer interactions provide a means for effectively decoupling the polymer motion from the dissipation of the liquid. Recent measurements of DNA/water relaxation times allow estimating numerical values in a parameterization of the decoupling effect. The resulting predicted frequency dependence explains many of the smaller features of Edwards' experiment as well as the overall anomaly. A simple model gives a surprisingly complete account of the features of the data using only values determined from other experiments.     

Why Structured Water Causes Sharp Absorption by DNA at Microwave Frequencies

Abstract

Aqueous solutions of oligopolymer DNA have been observed by G.S. Edwards, C.C. Davis, M.L. Swicord and J.D. Saffer, Phys. Rev. Lett. 53, 1284(1984) to show structured absorption of microwave energy in the region of several gigahertz, characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Although hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances, the molecular nature of the solvent in the near neighborhood of the polymer and - paradoxically- the strong water/polymer interactions provide a means for effectively decoupling the polymer motion from the dissipation of the liquid. Recent measurements of DNA/water relaxation times allow estimating numerical values in a parameterization of the decoupling effect. The resulting predicted frequency dependence explains many of the smaller features of Edwards' experiment as well as theoverall anomaly. A simple model gives a surprisingly complete account of the features of the data using only values determined from other experiments.     

The coelotrich: form and function of an unusual sensillum in Lowrya (Ostracoda: Myodocopina: Cypridinidae)

This study reports a previously undescribed and unique sensillum. Some species of Lowrya Parker 1998 (Ostracoda: Cypridinidae) possess sensillae of an unusual type arranged in a single row parallel to, and near, the anterior, ventral and posterior margins of the external surface of each carapace valve. These sensilla are here termed coelotrichs, and are each centred within an almost spherical cavity in the carapace. The cavity forms at the base of a depression, and the depression in turn lies within a sunken channel on the exterior carapace surface. The opening of the coelotrich cavity bears a 'plug', through which only the widened, divided base of a seta passes. The seta is very fine and stiff throughout most of its length, and exhibits no pores. For most of its length the seta is orientated parallel to the carapace surface, shielded within the sunken channel. The coelotrich is probably a velocity detector, acted upon by the viscous drag of the surrounding fluid. Its function is probably to detect vibrations in the substrate, such as acoustic motion in the surrounding liquid, or steady fluid drainage motion.     

Development of a noncontact and long-term respiration monitoring system using microwave radar for hibernating black bear

The aim of this study is to develop a prototype system for noncontact, noninvasive and unconstrained vital sign monitoring using microwave radar and to use the system to measure the respiratory rate of a Japanese black bear (Ursus thibetanus japonicus) during hibernation for ensuring the bear's safety. Ueno Zoological Gardens in Tokyo planned to help the Japanese black bear (female, approximately 2 years of age) going into hibernation. The prototype system has a microwave Doppler radar antenna (10-GHz frequency, approximately 7 mW output power) for measuring motion of the body surface caused by respiratory activity without making contact with the body. Monitoring using this system was conducted from December 2006 to April 2007. As a result, from December 18, 2006, to March 17, 2007, similar behaviors reported by earlier studies were observed, such as sleeping with curled up posture and not eating, urinating or defecating. During this hibernation period and also around the time of hibernation, the prototype system continuously measured cyclic oscillations. The presence of cyclic vibrations at 8-sec intervals (about 7 bpm) was confirmed by the system before she entered hibernation on December 3, 2006. The respiratory rate gradually decreased, and during the hibernation period the respiratory rate was extremely low at approximately 2 bpm with almost no change. The results show that motion on the body surface caused by respiratory activity can be measured without touching the animal's body. Thus, the microwave radar employed here can be utilized as an aid in observing vital signs of animals. Zoo Biol 28:259–270, 2009. © 2009 Wiley-Liss, Inc.     

Microwave assisted extraction of ursolic acid and oleanolic acid from Ocimum sanctum

Present study deals with the microwave assisted extraction (MAE) of ursolic acid (UA) and oleanolic acid (OA) from Ocimum sanctum leaves. UA and OA have been reported to possess significant medicinal properties. Various experimental parameters such as selection of solvent, solvent composition, irradiation time, microwave power, solid to solvent ratio, preleaching time and number of cycles were investigated to optimize the extraction process. Under optimum conditions of irradiation time (3 min), microwave power (272 W), solid to solvent ratio (1:30), preleaching time (10 min), maximum UA and OA has been extracted in one extraction cycle with ethanol: water (80:20) as a solvent. Maximum 86.76 and 89.64% of UA and OA was extracted under above mentioned optimized experimental conditions. MAE was also compared with the batch and ultrasound assisted extraction (UAE) method. As compared to batch and UAE, higher extraction yield of these important phytochemicals have been obtained through MAE in only 3 min.     

Thorax vibrations of a stingless bee (<Emphasis Type="Italic">Melipona seminigra</Emphasis>). I. No influence of visual flow

An important question in stingless bee communication is whether the thorax vibrations produced by foragers of the genus Melipona upon their return to the nest contain spatial information about food sources or not. As previously shown M. seminigra is able to use visual flow to estimate flight distances. The present study investigated whether foraging bees encode the visually measured distance in their thorax vibrations. Bees were trained to collect food in flight tunnels lined with a black-and-white pattern on their side walls and floor, which substantially influenced the image motion they experienced. When the bees had collected inside the tunnels the temporal pattern of their vibrations differed significantly from the pattern after collecting in a natural environment. These changes, however, were not associated with the visual flow experienced inside the tunnel. Bees collecting in tunnels offering little visual flow (stripes parallel to flight direction) modified their vibrations similarly to bees collecting in tunnels with high image motion (cross stripes). A higher energy expenditure due to drastically reduced flight velocities inside the tunnel is suggested to be responsible for changes in the thorax vibrations. The bees' vibrations would thus reflect the overall energetic budget of a foraging trip.     

Revising the Concept of Pore Hierarchy for Ionic Transport in Carbon Materials for Supercapacitors

Rapid motion of electrolyte ions is a crucial requirement to ensure the fast charging/discharging and the high power densities of supercapacitor devices. This motion is primarily determined by the pore size and connectivity of the used porous carbon electrodes. Here, the diffusion characteristics of each individual electrolyte component, that is, anion, cation, and solvent confined to model carbons with uniform and well‐defined pore sizes are quantified. As a result, the contributions of micropores, mesopores, and hierarchical pore architectures to the overall transport of adsorbed mobile species are rationalized. Unexpectedly, it is observed that the presence of a network of mesopores, in addition to smaller micropores—the concept widely used in heterogeneous catalysis to promote diffusion of sorbates—does not necessarily enhance ionic transport in carbon materials. The observed phenomenon is explained by the stripping off the surrounding solvent shell from the electrolyte ions entering the micropores of the hierarchical material, and the resulting enrichment of solvent molecules preferably in the mesopores. It is believed that the presented findings serve to provide fundamental understanding of the mechanisms of electrolyte diffusion in carbon materials and depict a quantitative platform for the future designing of supercapacitor electrodes on a rational basis.     

Insufficient hydrogen-bond desolvation and prion-related disease.

A structuring and eventual exclusion of water surrounding backbone hydrogen bonds takes place during protein folding as hydrophobic residues cluster around such bonds. Taken as an average over all hydrogen bonds, the extent of desolvation is nearly a constant of motion, as revealed by re-examination of the longest all-atom trajectory with explicit solvent [Y. Duan & P. A. Kollman (1998) Science 282, 740]. Furthermore, this extent of desolvation is preserved across native soluble proteins, except for cellular prion proteins. Thus, a physico-chemical picture of prion-related disease emerges. The epitope for protein-X binding, the region undergoing vast conformational change and the trigger and locker for this change are inferred from the location of under-desolvated hydrogen bonds in the cellular prion protein.     

Persistence of past stimulations: storing sounds within the inner ear

Tones cause vibrations within the hearing organ. Conventionally, these vibrations are thought to reflect the input and therefore end with the stimulus. However, previous recordings of otoacoustic emissions and cochlear microphonic potentials suggest that the organ of Corti does continue to move after the end of a tone. These after-vibrations are characterized here through recordings of basilar membrane motion and hair cell extracellular receptor potentials in living anesthetized guinea pigs. We show that after-vibrations depend on the level and frequency of the stimulus, as well as on the sensitivity of the ear. Even a minor loss of hearing sensitivity caused a sharp reduction in after-vibration amplitude and duration. Mathematical models suggest that after-vibrations are driven by energy added into organ of Corti motion after the end of an acoustic stimulus. The possible importance of after-vibrations for psychophysical phenomena such as forward masking and gap detection are discussed.     

Microwave‐assisted extraction of total bioactive saponin fraction from Gymnema sylvestre with reference to gymnemagenin: a potential biomarker

Objective – To develop a fast and ecofriendly microwave assisted extraction (MAE) technique for the effective and exhaustive extraction of gymnemagenin as an indicative biomarker for the quality control of Gymnema sylvestre. Methodology – Several extraction parameters such as microwave power, extraction time, solvent composition, pre‐leaching time, loading ratio and extraction cycle were studied for the determination of the optimum extraction condition. Scanning electron micrographs were obtained to elucidate the mechanism of extraction Results – The final optimum extraction conditions as obtained from the study were: 40% microwave power, 6 min irradiation time, 85% v/v methanol as the extraction solvent, 15 min pre‐leaching time and 25 : 1 (mL/g) as the solvent‐to‐material loading ratio. The proposed extraction technique produced a maximum yield of 4.3% w/w gymnemagenin in 6 min which was 1.3, 2.5 and 1.95 times more efficient than 6 h of heat reflux, 24 h of maceration and stirring extraction, respectively. A synergistic heat and mass transfer theory was also proposed to support the extraction mechanism Conclusion – Comparison with conventional extraction methods revealed that MAE could save considerable amounts of time and energy, whilst the reduction of volume of organic solvent consumed provides an ecofriendly feature. Copyright © 2009 John Wiley & Sons, Ltd.     

A model for water motion in crystals of lysozyme based on an incoherent quasielastic neutron-scattering study

This paper reports an incoherent quasielastic neutron scattering study of the single particle, diffusive motions of water molecules surrounding a globular protein, the hen egg-white lysozyme. For the first time such an analysis has been done on protein crystals. It can thus be directly related and compared with a recent structural study of the same sample. The measurement temperature ranged from 100 to 300 K, but focus was on the room temperature analysis. The very good agreement between the structural and dynamical studies suggested a model for the dynamics of water in triclinic crystals of lysozyme in the time range approximately 330 ps and at 300 K. Herein, the dynamics of all water molecules is affected by the presence of the protein, and the water molecules can be divided into two populations. The first mainly corresponds to the first hydration shell, in which water molecules reorient themselves fivefold to 10-fold slower than in bulk solvent, and diffuse by jumps from hydration site to hydration site. The long-range diffusion coefficient is five to sixfold less than for bulk solvent. The second group corresponds to water molecules further away from the surface of the protein, in a second incomplete hydration layer, confined between hydrated macromolecules. Within the time scale probed they undergo a translational diffusion with a self-diffusion coefficient reduced approximately 50-fold compared with bulk solvent. As protein crystals have a highly crowded arrangement close to the packing of macromolecules in cells, our conclusion can be discussed with respect to solvent behavior in intracellular media: as the mobility is highest next to the surface, it suggests that under some crowding conditions, a two-dimensional motion for the transport of metabolites can be dominant.     

Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1

Studies using time-resolved fluorescence depolarization were performed on the internal motion of Trp 59 of ribonuclease T1 (EC 3.1.27.3) in the free enzyme, 2'-GMP-enzyme complex and 3'-GMP-enzyme complex. The Trp 59 motion was also studied in the free enzyme using molecular dynamics simulations. Energetic analysis of activation barriers to the Trp 59 motion was performed using both the transition state theory and Kramers' theory. The activation parameters showed a dependence on solvent viscosity indicating the transition state approach in aqueous solution to be inadequate. When taking solvent viscosity contributions into account agreement between the transition state and Kramers' theories was obtained. The results indicate the three enzyme forms to have different conformations with the free enzyme and 3'-GMP-enzyme complex being similar. Comparison of the experimental and theoretical results showed a good agreement on the Trp 59 motion in the free enzyme. Trp 59 appears to vibrate rapidly, with a relaxation time of the order of 1 ps, within free space in the protein matrix and to have a slower motion, with a relaxation time of the order of 100 ps, which is related to breathing of the surrounding protein matrix. Molecular dynamics results indicate high mobility in regions of the enzyme involved in the interaction with the guanine base of the inhibitor or substrate while much lower mobility occurred in residues involved in the catalytic mechanism of ribonuclease T1.     

密闭微波辅助间歇提取RP-HPLC测定三七中三种皂苷类化合物

本文建立了采用微波辅助间歇提取三七样品中的皂苷类化合物,并以反相高效液相色谱（RP—HPLC）测定其中三七皂苷R1、人参皂苷Rg1和人参皂苷Rb1含量的实验方法。分别通过单因素实验和正交实验设计,优化了萃取溶剂浓度、溶剂用量、微波功率和微波辐射时间等提取条件。与传统的索氏提取法、冷浸法和超声波提取法比较,微波辅助萃取法具有快速、提取率高、溶剂消耗少等优点,间歇萃取较连续萃取更是大大节省了微波能耗。     

An efficient, simple and expedition synthesis of 1-amidoalkyl-2-naphthols as 'drug like' molecules for biological screening

An efficient and direct protocol for the preparation of amidoalkyl naphthols employing a multi-component, one-pot condensation reaction of beta-naphthol, aromatic aldehydes and acetamide in the presence of ferric hydrogensulfate under solvent, solvent-free and microwave conditions is described. The thermal solvent-free and microwave green procedures offer advantages such as shorter reaction times, simple work-up, excellent yield, recovery and reusability of catalyst. It is noteworthy that 1-amidomethyl-2-naphthols can be converted into important biological 'drug like' active 1-aminomethyl-2-naphthols derivatives by amide hydrolysis.     

Protein dynamics viewed by hydrogen exchange

To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the backbone amide hydrogens of Staphylococcal nuclease was compared with that of their neighbors, with their structural environment, and with other information. Results show that H-bonded hydrogens are protected from exchange, with HX rate effectively zero, even when they are directly adjacent to solvent. The transition to exchange competence requires a dynamic structural excursion that removes H-bond protection and allows exposure to solvent HX catalyst. The detailed data often make clear the nature of the dynamic excursion required. These range from whole molecule unfolding, through smaller cooperative unfolding reactions of secondary structural elements, and down to local fluctuations that involve as little as a single peptide group or side chain or water molecule. The particular motion that dominates the exchange of any hydrogen is the one that allows the fastest HX rate. The motion and the rate it produces are determined by surrounding structure and not by nearness to solvent or the strength of the protecting H-bond itself or its acceptor type (main chain, side chain, structurally bound water). Many of these motions occur over time scales that are appropriate for biochemical function.     

How Moving Backgrounds Influence Interception

Reaching movements towards an object are continuously guided by visual information about the target and the arm. Such guidance increases precision and allows one to adjust the movement if the target unexpectedly moves. On-going arm movements are also influenced by motion in the surrounding. Fast responses to motion in the surrounding could help cope with moving obstacles and with the consequences of changes in one’s eye orientation and vantage point. To further evaluate how motion in the surrounding influences interceptive movements we asked subjects to tap a moving target when it reached a second, static target. We varied the direction and location of motion in the surrounding, as well as details of the stimuli that are known to influence eye movements. Subjects were most sensitive to motion in the background when such motion was near the targets. Whether or not the eyes were moving, and the direction of the background motion in relation to the direction in which the eyes were moving, had very little influence on the response to the background motion. We conclude that the responses to background motion are driven by motion near the target rather than by a global analysis of the optic flow and its relation with other information about self-motion.     

微波萃取苦荞壳中总黄酮工艺研究

本文在提取苦荞壳中总黄酮的工艺实验中,优化了提取溶剂的种类,水和乙醇,同时还使用了超声波和微波辅助提取,并分别将不同因素,如溶剂种类及浓度,提取时间,温度,pH,液固比等,对提取结果的影响作了比较,结果表明,当介质为乙醇时的微波萃取效果明显优于其他提取方法。     

Dynamics of electron transfer pathways in cytochrome C oxidase

Cytochrome c oxidase mediates the final step of electron transfer reactions in the respiratory chain, catalyzing the transfer between cytochrome c and the molecular oxygen and concomitantly pumping protons across the inner mitochondrial membrane. We investigate the electron transfer reactions in cytochrome c oxidase, particularly the control of the effective electronic coupling by the nuclear thermal motion. The effective coupling is calculated using the Green's function technique with an extended Huckel level electronic Hamiltonian, combined with all-atom molecular dynamics of the protein in a native (membrane and solvent) environment. The effective coupling between Cu(A) and heme a is found to be dominated by the pathway that starts from His(B204). The coupling between heme a and heme a(3) is dominated by a through-space jump between the two heme rings rather than by covalent pathways. In the both steps, the effective electronic coupling is robust to the thermal nuclear vibrations, thereby providing fast and efficient electron transfer.     

Dynamics of hydrogen bond desolvation in protein folding

As proteins fold, a progressive structuring, immobilization and eventual exclusion of water surrounding backbone hydrogen bonds takes place. This process turns hydrogen bonds into major determinants of the folding pathway and compensates for the penalty of desolvation of the backbone polar groups. Taken as an average over all hydrogen bonds in a native fold, this extent of protection is found to be nearly ubiquitous. It is dynamically crucial, determining a constraint in the long-time limit behavior of coarse-grained ab initio simulations. Furthermore, an examination of one of the longest available (1micros) all-atom simulations with explicit solvent reveals that this average extent of protection is a constant of motion for the folding trajectory. We propose how such a stabilization is best achieved by clustering five hydrophobes around the backbone hydrogen bonds, an arrangement that yields the optimal stabilization. Our results support and clarify the view that hydrophobic surface burial should be commensurate with hydrogen-bond formation and enable us to define a basic desolvation motif inherent to structure and folding dynamics.