Mechanism of the stabilization of ribonuclease A by sorbitol: preferential hydration is greater for the denatured then for the native protein.

The effect of interactions of sorbitol with ribonuclease A (RNase A) and the resulting stabilization of structure was examined in parallel thermal unfolding and preferential binding studies with the application of multicomponent thermodynamic theory. The protein was stabilized by sorbitol both at pH 2.0 and pH 5.5 as the transition temperature, Tm, was increased. The enthalpy of the thermal denaturation had a small dependence on sorbitol concentration, which was reflected in the values of the standard free energy change of denaturation, delta delta G(o) = delta G(o) (sorbitol) - delta G(o)(water). Measurements of preferential interactions at 48 degrees C at pH 5.5, where protein is native, and pH 2.0 where it is denatured, showed that sorbitol is preferentially excluded from the denatured protein up to 40%, but becomes preferentially bound to native protein above 20% sorbitol. The chemical potential change on transferring the denatured RNase A from water to sorbitol solution is larger than that for the native protein, delta mu(2D) > delta mu(2N), which is consistent with the effect of sorbitol on the free energy change of denaturation. The conformity of these results to the thermodynamic expression of the effect of a co-solvent on denaturation, delta G(o)(W) + delta mu(D)(2)delta G(o)(S) + delta mu(2D), indicates that the stabilization of the protein by sorbitol can be fully accounted for by weak thermodynamic interactions at the protein surface that involve water reversible co-solvent exchange at thermodynamically non-neutral sites. The protein structure stabilizing action of sorbitol is driven by stronger exclusion from the unfolded protein than from the native structure.     

Design of interacting multi-stable nucleic acids for molecular information processing

Despite an exponential increase in computing power over the past decades, present information technology falls far short of expectations in areas such as cognitive systems and micro robotics. Organisms demonstrate that it is possible to implement information processing in a radically different way from what we have available in present technology, and that there are clear advantages from the perspective of power consumption, integration density, and real-time processing of ambiguous data. Accordingly, the question whether the current silicon substrate and associated computing paradigm is the most suitable approach to all types of computation has come to the fore. Macromolecular materials, so successfully employed by nature, possess uniquely promising properties as an alternate substrate for information processing. The two key features of macromolecules are their conformational dynamics and their self-assembly capabilities. The purposeful design of macromolecules capable of exploiting these features has proven to be a challenge, however, for some groups of molecules it is increasingly practicable. We here introduce an algorithm capable of designing groups self-assembling of nucleic acid molecules with multiple conformational states. Evaluation using natural and artificially designed nucleic acid molecules favours this algorithm significantly, as compared to the probabilistic approach. Furthermore, the thermodynamic properties of the generated candidates are within the same approximation as the customised trans-acting switching molecules reported in the laboratory.     

Transition state stabilization of subtilisins in organic media

Electrostatic forces are among the stabilizing interactions that contribute to the high degree of enzyme-transition state complementarity. The active-site polarity, which can differ substaintially from that of water, is thus an important determinant of transition state stabilization. Here we pose the question of whether the rate of an enzymatic reaction proceeding through a charged transition state can be increased by increasing the active-site polarity in an organic solvent. The active-site polarity of subtilisin has been reduced by dehydration and suspension in a nonpolar solvent (tetrahydrofuran), and then increased by adding water to the solvent. Enhancing the local polarity substantially increasing the rate of catalysis, implicating polarity as an important factor in stabilizing the charged tetrahedral transition state. Studies with subtilisins whose active sites have been modified by site-directed mutagenesis support the role of polarity in transition state stabilization. (c) 1994 John Wiley & Sons, Inc.     

Inositol phosphates compete with nucleic acids for binding to bovine leukemia virus matrix protein: Implications for deltaretroviral assembly

The matrix (MA) domain of retroviral Gag proteins plays a crucial role in virion assembly. In human immunodeficiency virus type 1 (HIV‐1), a lentivirus, the presence of phosphatidylinositol‐(4,5)‐bisphosphate triggers a conformational change allowing the MA domain to bind the plasma membrane (PM). In this study, the MA protein from bovine leukemia virus (BLV) was used to investigate the mechanism of viral Gag binding to the membrane during replication of a deltaretrovirus. Fluorescence spectroscopy was used to measure the binding affinity of MA for two RNA constructs derived from the BLV genome as well as for single‐stranded DNA (ssDNA). The importance of electrostatic interactions and the ability of inositol hexakisphosphate (IP6) to compete with nucleic acids for binding to MA were also investigated. Our data show that IP6 effectively competes with RNA and DNA for BLV MA binding, while [NaCl] of greater than 100 mM is required to produce any observable effect on DNA‐MA binding. These results suggest that BLV assembly may be highly dependent on the specific interaction of the MA domain with components of the PM, as observed previously with HIV‐1. The mode of MA binding to nucleic acids and the implications for BLV assembly are discussed. Proteins 2013; 81:1377–1385. © 2013 Wiley Periodicals, Inc.     

Changes in the metabolism of nucleic acids during the growth and senescence of tobacco callus

Changes in DNA and RNA metabolism, DNA composition and RNA species in callus of tobacco ( Nicotiana rustica L. cv. Gansu Yellow Flower) were investigated during the growth and senescence. DNA and RNA contents remained almost unchanged during the callus growth period, but started to decrease synchronously at the time that callus senescence was initiated. Synthesis of DNA and RNA, as measured by incorporation of [³H]-labelled precursor, increased during the growth period and did not decrease until late in senescence. The activities of DNase and RNase (pH 4.5) increased during the early senescence period in accordance with the decrease in the levels of DNA and RNA, but appeared to decrease during late senescence. These results suggest that the decrease in the levels of DNA and RNA in senescing tobacco callus may stem from the increase in the hydrolytic activities of DNase and RNase (pH 4.5) in the early stage of senescence, and that the slowdown of synthesis in the late senescence period may also be a cause. DNA and RNA electrophoresis showed that a low-molecular-weight satellite DNA band disappeared after the onset of senescence and that the nuclear main band DNA gradually decreased, whereas the high-molecular-weight satellite DNA seemed to undergo no significant changes during the senescence period tested. Of the RNA species, 4–5S RNA was far more susceptible to damage during senescence than 25S and 18S rRNA. This suggests different susceptibilities of different DNA and RNA components to damage during the senescence of tobacco callus or alternatively a highly sequenced degradation of DNA and RNA molecules.     

First experimental evidence for female mate choice in a nocturnal primate

Female mate choice can be hypothesised in most nocturnal primates, since females show a higher investment in their offspring than males. The aim of this experimental study was to investigate if female grey mouse lemurs perform mate choice and whether age, relatedness (to the male), or male advertisement call activity systematically influence their decisions. A two-way mate choice design was developed in which females could choose between two males. Mate choice was deduced from the time spent in proximity to the males and from mating behaviour. During oestrus 12 of 17 females participated actively in the experiment and all of them showed either a significant spatial (n=11) or behavioural (n=1) preference for one male. In four cases copulations were observed. The influence of age on female mate choice was not statistically significant. In the cases with copulations, however, females mostly preferred the older male. This might indicate a preference for older age as an indicator of experience, fitness, and/or status. The influence of relatedness on female mate choice could not be definitely clarified. However, results imply a mechanism of kin recognition on the basis of familiarity. In the majority of choices, females preferred the male with higher trill call activity. Since trill call activity correlates with the relative dominance status of males, these results suggest an importance of the male dominance status for female mate choice in grey mouse lemurs. Altogether our findings indicate that females use a complex of different cues to choose their mates.     

Effects of copper deficiency on pollen fertility and nucleic acids in the durum wheat anther

Summary The effects of continuous copper deficiency and of temporary deficiencies initiated prior to (initial deficiency) or after (terminal deficiency) the end of tillering (a stage preceding the meiotic cycle) on pollen formation were investigated in durum wheat grown on a nutrient solution. The effects of the treatments on pollen viability (FCR test) and on the proline content of the pollen grains suggested that copper deficiency induced a nearly complete sterility of the pollen formed and inhibited all grain production. Temporary copper deficiencies significantly reduced the viability rate and the number of proline-rich pollen grains without affecting pollengrain production. Cytophotometric measurements showed that initial copper deficiency induced a significant increase in the proportion of polyploid microspore mother cells (MMCs), whereas terminal copper deficiency blocked endomitotic DNA syntheses. Protein metabolism was markedly altered by the treatments. The RNA content of the cytoplasm of tapetum cells was decreased by 34%–48%, depending on the treatment. The autoradiographic study showed that the stress caused by copper deficiency enhanced [³H]uridine incorporation into microspore cytoplasm RNA and also into the tapetum cells in the case of temporary deficiencies. The incidence of the treatments on the ploidy of the mother cells and on the disturbance of protein metabolism, particularly in tapetum cells, is discussed.     

Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13 years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen’s WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion’s RecoverAll method recovered the most amplifiable RNA.     

Localization of nucleic acids in the nucleoli of oocytes and early embryos of mouse and hamster: An autoradiographic study

Mouse preovulatory oocytes, zygotes, parthenogenetically activated pronuclear oocytes, and early embryos, as well as hamster zygotes, were analyzed, by autoradiography, for the distribution of either “maternal” or newly synthesized RNAs. Early mouse embryos were also examined for the distribution of newly replicated DNA. Special attention was attributed to NLBs in oocytes or to NPBs in early embryos. In mouse oocytes, [5-³H]uridine radioactivity accumulated (after a 2-hr pulse) in vitro, in addition to other nuclear compartments, in the central compact material of the NLBs. There was no cytoplasmic labeling. In all parthenogenetic pronuclear embryos developed from similarly labeled oocytes, this label was distinctly detectable in the central compact material of the NPBs; less intensive labeling was seen in the nucleoplasm and cytoplasm. On the contrary, the central compact part of the mouse NPB did not show labeling in DNA after a continuous culture with [6-³H]thymidine. In mouse and hamster pronuclear zygotes, convincing evidence was obtained for a lack of any newly synthesized nucleic acids in the compact material of NPBs using 4- to 10-hr culture with [8-³H]adenosine. Based on these data, it was shown that the NLBs of oocytes or NPBs of early embryos probably contain RNAs synthesized during the last stages of antral follicle oocyte differentiation. This unique pathway of RNAs in the oocyte—embryo system may explain the specific morphology of both oocyte and early embryo “nucleoli.” © 1995 Wiley-Liss, Inc.     

Studies on the retention of plasmid DNA and Escherichia coli nucleic acids by hydrophobic interaction chromatography

This work presents studies on the interactions of supercoiled plasmid DNA and Escherichia coli genomic DNA (gDNA) and RNA, with an hydrophobic interaction chromatography (HIC) gel, obtained by derivatisation of Sepharose CL-6B with 1,4-butanediol diglycidyl ether. Nucleic acids purified from E. coli were injected separately in the above HIC column and eluted with 1.5 M (NH₄)₂SO₄ in the buffer. The column was able to separate single-stranded from double-stranded nucleic acids. RNA and denatured gDNA were retarded in a different way due to the interactions of the exposed hydrophobic bases with the ligands. Supercoiled plasmid DNA, on the contrary, eluted in the flowthrough. This revised version was published online in July 2006 with corrections to the Cover Date.     

Passive and active stabilization of dopamine in the striatum

Parkinson's disease is a neurodegenerative disorder associated with cell loss from the substantia nigra pars compacta (SNc). The dopaminergic cells of the SNc project to the striatum where the loss of dopaminergic tone is thought to be the main cause of Parkinsonism symptoms. Animal models have shown that striatal tissue content of dopamine declines proportionally to cell death in the SNc but the extracellular concentration of dopamine (EDA) in the striatum remains near normal until more than 85% of SNc neurons have died. We investigate various explanations for the remarkable homeostasis of EDA with a mathematical model that has recently been constructed for dopamine synthesis, release, and reuptake, which includes the effects of the autoreceptors. We provide evidence and explanations for the passive stabilization hypothesis and show that the autoreceptors enhance stabilization of EDA only when fewer than 25% of the SNc cells remain.     

重金属污染土壤稳定/固化修复技术研究进展

修复重金属污染土壤一直是国际上的难点和热点研究课题.目前常用的污染场地修复技术主要包括挖掘、稳定/固化(solidification/stabilization,S/S)、化学淋洗、气提、热处理、生物修复等.本文在参考美国环境保护署(EPA)、英国环境署的S/S技术规范、国内外发明专利基础上,对S/S的概念、国内外发展现状及今后的发展方向进行了系统论述.固定化技术通过把污染物囊封入惰性基材中,或在污染物外面加上低渗透性的材料,来减少污染物暴露的淋滤面积以达到限制污染物迁移的目的.稳定化技术是从改变污染物的有效性出发,将污染物转化为不易溶解、迁移能力或毒性更小的形式.S/S技术包括:水泥固化、石灰火山灰固化、塑性材料包容固化、玻璃化技术、药剂稳定化.在稳定化技术中,加入药剂的目的是改变土壤的物理、化学性质,通过pH控制技术、氧化还原电势技术、沉淀技术、吸附技术、离子交换技术等改变重金属在土壤中的存在状态,从而降低其生物有效性和迁移性.本文还论述了S/S修复效果评价方法,并指出需加强S/S技术中的分子键合技术、土聚合物以及我国的S/S技术导则制定等工作.     

Studies of the retrogradation process for various starch gels using Raman spectroscopy

The retrogradation of untreated wild-type starches (potato, maize, and wheat), waxy maize starches, and one pregelatinized, modified amylose-rich starch was investigated continuously using Raman spectroscopy. The method detects conformational changes due to the multi-stage retrogradation, the rate of which differs between the starches. The pregelatinized, modified amylose-rich starch shows all stages of retrogradation in the course of its Raman spectra. In comparison to amylose, the retrogradation of amylopectin is faster at the beginning of the measurements and slower in the later stages. The untreated starches can be ranked in the order of their rate of retrogradation as follows: potato>maize>wheat.     

Development and in vivo testing of a high frequency endoscopic Raman spectroscopy system for potential applications in the detection of early colonic neoplasia

The objective of this study was to build and test an adjunct system to a colonoscope for in vivo measurement of Raman spectra from colon tissue for potentially improving the detection of early cancers. The novelty of this system was that low cost fibre optic probes were used, without the addition of expensive optical filters. Good quality in vivo Raman spectra were successfully obtained with a 1 s integration time in the high frequency (HF) range from normal tissue and polyps of patients during a colonoscopy. The polyps were subsequently removed, and their pathology determined. The acquired in vivo Raman spectra showed clear changes between tissue with normal and tubular adenoma pathology. Further clinical study with this low cost HF Raman probe is warranted to fully test its clinical utility.

Left: Raman probe orientated on a suspected polyp (indicated by arrow) under video surveillance during a colonoscopy. Right: average Raman spectra from 2800–3050 cm^–1 obtained from polyps at different stages of disease. The peak intensities are in arbitrary units.     

Raman spectroscopy as a non‐invasive technique for the quantification of melanins in feathers and hairs

The quantification of melanins is a complex task due to the chemical heterogeneity of the pigments and the difficulty of their isolation. The best accepted procedure currently consists in the chemical cleavage of melanins and the subsequent detection of degradation products by HPLC, which implies the destruction of samples. Here, we show that Raman spectroscopy is a non‐invasive technique that can be used to quantify melanins. We made parallel analyses of the characteristics of pheomelanin and eumelanin Raman spectra as measured by confocal Raman microscopy and of degradation products of pheomelanin (4‐amino‐3‐hydroxyphenylalanine, 4‐AHP) and eumelanin (pyrrole‐2,3,5‐tricarboxylic acid, PTCA) as measured by HPLC in feathers of red‐legged partridges and hairs of wild boars and humans. We found strong correlations between the spectral Raman characteristics and 4‐AHP and PTCA levels, which indicates that the Raman spectra of melanins can be used to determine their content.     

Spectroscopic evidence revealing polyproline II structure in hydrophobic, putatively elastomeric sequences encoded by specific exons of human tropoelastin

Elastin, the protein responsible for tissue elasticity, is contained in arterial walls, lungs, and skin. Given the cassette like organization of the human tropoelastin gene, giving rise to alternating exons encoding for crosslink domains and elastomeric domains, it is tempting to suggest that polypeptides encoded by different exons could adopt structures independent of the other exons. The results obtained with the polypeptide sequences encoded by exons 3, 7, and 30 of human tropoelastin are described. It is shown that these hydrophobic exons may partly assume the polyproline II (PPII) structure, as found by circular dichroism studies in aqueous solution. Classical Raman spectroscopy evidences a specific sharp band at 1314 cm(-1), which is assigned to the PPII structure adopted by these exons in the solid state. As these sequences are among those putatively responsible for elastomeric properties, these findings are of particular interest in relation to the current models of the elasticity of elastin.     

Adsorption and elution characteristics of nucleic acids on silica surfaces and their use in designing a miniaturized purification unit

We report nucleic acid (NA) adsorption isotherms and elution profiles for silica surfaces and use these to design a miniaturized NA purification unit based on solid-phase extraction with silica beads. The procedure is based on a pressure drop equation for flow through a packed bed and allows estimation of key design parameters such as channel dimensions, liquid flow rates, sample volume, and amount of silica needed. The usefulness of this design procedure is demonstrated by applying it to a column-based NA purification device for influenza detection for a case study of Madin-Darby canine kidney cells infected with influenza A virus.