红树林对水体净化作用研究进展

红树是一类生长在热带及亚热带海岸潮间带的湿地植物,具有净化水体的功能。近年来红树林净化水体方面的研究有不少进展,主要包括促进水体中悬浮物的沉降,利用其丰富的底栖生物对有机物的吸附和降解,以及其植株和底泥对重金属和营养盐的富集和吸收。但是红树林的净化容量是有限的,超负荷的污水排放会导致明显的或潜在的生态风险。在实际应用中,只有在充分的监控和限制条件下,才可有限地将红树林作为生活污水排放地。该研究的发展方向主要有污染物迁移转化过程中各因素的相互作用、红树林的对环境的综合改善能力以及实际应用中对生态风险的量化分析和监测等几方面。     

Preparation of photosystem I particles from spinach by column chromatography

Photosystem I (PS I) particles were prepared from spinach leaves by a method which includes two different types of chromatographies: an ion-exchange DEAE-Toyopearl column and a hydrophobic Butyl-Toyopearl column. Potassium ferricyanide was added to the preparation media in the early steps of preparation. The addition of ferricyanide protected iron-sulfur centers from damage due to photoinactivation during preparation and preserved some unknown polypeptides on the isolated PS I. Consequently, the PS I particles isolated by the present method showed a very high activity in the NADP-photoreduction of 388 mol NADP reduced/mg Chl/hr.This paper was presented at the Japan-US Binational Seminar on Solar Energy Conversion at Okazaki, Japan, March 17–21, 1987.     

Control of oligonucleotide retention on a pH-stabilized strong anion exchange column

Strong anion exchange columns are preferred for oligonucleotide analyses due to their ability to effectively control secondary structure and poly(G) interactions. Methacrylate-based anion exchange phases minimize hydrophobic interactions with oligonucleotides, but they also tend to hydrolyze under alkaline conditions. In this article, we report the use of an anion exchange column prepared from a new class of methacrylate monomers designed to improve hydrolytic stability. This column is used to show predictable adjustment of oligonucleotide retention by eluent pH and composition. Features of the new column include (i) large, predictable, pH-dependent retention shifts (varying with specific changes in 5' or 3' terminal bases with NaCl-based eluents); (ii) reduced retention when solvent is added to NaCl-based eluents; and (iii) suppression of much of the column's hydrophobic interactions when CH3CN is used with NaClO4-based eluents at a neutral pH (i.e., this eluent system separates oligonucleotides primarily in order of their length). These observations will aid the development of elution conditions for both size-dependent and base sequence-dependent (or base composition-dependent) separations.     

Synaptic processes in the neurons of Clarke's column evoked by an antidromic volley from the dorsolateral column

In cats under nembutal-chloralose anaesthesia we investigated the response of neurons of Clarke's column to stimulation of axons ascending in the dorsal part of the lateral funiculus. Excitation of the descending fibers of the funiculus was prevented either by an ipsilateral hemisection of the thoracic cord carried out 7–10 days previously, which caused them to degenerate, or by stimulation of ascending axons in the region of the restiform bodies. It was found that with both kinds of stimulation records could be obtained from neurons in Clarke's column in which a descending volley causes not antidromic action potentials but primary excitatory postsynaptic potentials (EPSP). The length of the latent period of the EPSP (10–15 msec) suggests that they are monosynaptic. Such neurons may also be activated by low- or high-threshold afferents from various muscles; evidently they correspond to those described by Retheyi [14] as "edge" neurons on which terminate collaterals of axons ascending in the dorsal spinocerebellar tract (DSCT). In some of the neurons of the DSCT whose axons are distinguished by a low conduction velocity, stimulation of the dorsolateral funiculus caused not only antidromic spikes but also EPSP's following after them, and it would seem that the "edge" neurons were involved in their formation. We consider the possible functional role of a negative feed back loop formed by axon collaterals of neurons of the DSCT and by the "edge" neurons.A. A. Bogomolets Institute of Physiology, Academy of Sciences of the Ukrainian SSR, Kiev. Translated from Neirofiziologiya, Vol. 2, No. 3, pp. 269–278, May–June, 1970.     

Protein topology from predicted residue contacts

Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.     

Solvent modulation of column chromatography

A majority of column chromatographies use only selected salts, e.g., ammonium sulfate, NaCl, Citrate and phosphate in hydrophobic interaction chromatography (HIC) and NaCl in ion exchange and dye affinity chromatographies. Alternatively, a pH range below or above the neutral value is often used to reduce affinity interactions, e.g., in Protein-A or dye affinity column chromatography. Although these parameters are easily manipulated, they are not necessarily the optimal conditions for high recovery and resolution of the proteins. So-called co-solvents have been used, although to a limited extent, to manipulate performance of column chromatography. Here the term co-solvent is used to indicate its relatively high concentrations required for these applications, meaning that it also serves as solvent along with water. Ethylene glycol and MgCl(2) have been used to elute specific antibodies from antigen-affinity column. Arginine has also been used for the same purpose. Arginine has much wider applications for various column chromatographies, including size exclusion chromatography (SEC), HIC and affinity chromatography. Polyethylene glycol and glycine have also been used to improve the performance of HIC and hydroxyapatite chromatography. This review summarizes these applications of co-solvents for column chromatographies.     

Electrostatically driven lipid–protein interaction: Answers from FRET

Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein–lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques.In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid–protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid–protein interactions.     

Separation of large unilamellar liposomes from blood components by a spin column procedure: towards identifying plasma proteins which mediate liposome clearance in vivo.

In order to facilitate the isolation of liposomes from blood components, we have developed a simple and rapid procedure combining chromatographic and centrifugal methods. This 'spin column' procedure was used to isolate liposomes from incubation mixtures with human serum or from the blood of CD1 mice after intravenous administration of liposomes. An advantage of this procedure is that processing times are fast (typically minutes) such that the isolation procedure can be done in the absence of chelators or other coagulation inhibitors which may affect protein/liposome interactions. Furthermore, several samples can be analyzed together and small sample volumes can be processed. In addition, we show that this spin column procedure can be employed to isolate large unilamellar vesicles averaging 100 nm in diameter from lipoproteins and plasma proteins. The applicability of this spin column procedure in studying protein/liposome interactions is demonstrated by quantitating the amount of human complement component C3 bound per liposome using a C3 competitive ELISA assay after incubation with human serum. The proteins associated with the recovered liposomes were further analyzed by conventional SDS-polyacrylamide gel electrophoresis. We show that egg phosphatidylcholine/cholesterol (55:45, mol/mol) or egg phosphatidylcholine/cholesterol/dioleoylphosphatidylserine (35:45:20, mol/mol) liposomes isolated from the circulation of CD1 mice within minutes of administration have distinct, complex profiles of associated proteins. By isolating circulating large unilamellar liposomes using the spin column method and characterizing the proteins associated with their membranes, this protein fingerprinting approach will expedite identifying protein interactions which affect liposome stability and clearance in vivo.     

Learning to predict protein-protein interactions from protein sequences

In order to understand the molecular machinery of the cell, we need to know about the multitude of protein-protein interactions that allow the cell to function. High-throughput technologies provide some data about these interactions, but so far that data is fairly noisy. Therefore, computational techniques for predicting protein-protein interactions could be of significant value. One approach to predicting interactions in silico is to produce from first principles a detailed model of a candidate interaction. We take an alternative approach, employing a relatively simple model that learns dynamically from a large collection of data. In this work, we describe an attraction-repulsion model, in which the interaction between a pair of proteins is represented as the sum of attractive and repulsive forces associated with small, domain- or motif-sized features along the length of each protein. The model is discriminative, learning simultaneously from known interactions and from pairs of proteins that are known (or suspected) not to interact. The model is efficient to compute and scales well to very large collections of data. In a cross-validated comparison using known yeast interactions, the attraction-repulsion method performs better than several competing techniques.     

Application of short column gel permeation in the study of protein-protein interactions

A simple and rapid procedure based on the gel filtration principle is described together with its applicability to the study of protein-protein interactions including subunit-subunit and enzyme-enzyme interactions. Using this procedure, it is shown that phosphoglycerate kinase (PGK) and glyceraldehyde-3-phosphate dehydrogenase (GPDH) interact with a stoichiometry of one PGK molecule combining with one monomeric subunit of GPDH. This interaction has been observed with both enzymes being from the same, as well as from different, species. The K_d values for rabbit muscle PGK and porcine muscle GPDH complex and that for the rabbit muscle PGK and yeast GPDH complex are found to be (4.5 ± 2.0) × 10⁻⁷ M and (6.5 ± 1.7) × 10⁻⁷ M, respectively. The specificity of bienzyme association is stronger when enzymes are from the same species than when they are from different species.     

Purification of D-alanine carboxypeptidase from Escherichia coli B on a penicillin-Sepharose column.

1. A soluble D-alanine carboxypeptidase from Escherichia coli strain B was purified on a p-aminobenzylpenicillin-Sepharose column. This one-step chromatography followed by an (NH4)2SO4 precipitation yielded an enzyme purified 1200-fold and some of its properties are reported. 2. The pure D-alanine carboxypeptidase was devoid of D-alanine carboxypeptidase II activity and migrated as a single protein band on analytical disc gel electrophoresis. 3. Triton X-100 in the purification procedure is an absolute requirement for obtaining a stable enzyme. 4. The enzymic activity of D-alanine carboxypeptidase was greatly affected in solution of high salt concentrations and varied somewhat with the nature of the cation tested.     

Sharing the water column: physiological mechanisms underlying species-specific habitat use in tunas

Tuna species support some of the world’s largest commercial and recreational fisheries. Their extensive migratory patterns expose them to multiple national and international fisheries and fishery management regimes. Several prized species have become the focus of global conservation efforts and there is a growing worldwide interest in establishing optimal strategies for sustainable tuna fisheries. Although this task has proven to be very challenging, it has taken on a new sense of urgency in the face of the potential effects of global climate change. A better understanding of the interactions between environmental conditions and tuna physiology and how they affect tuna behavior will offer population and stock assessment modelers and fisheries biologists a more mechanistic understanding of tuna distribution patterns and may help predict changes in both geographic and depth-related movement patterns. Indeed, physiological data comprise a growing component of multi-trait analysis approaches to species conservation. Our review aims to summarize what is known about differences among tuna species in distribution patterns, tolerances to environmental conditions, and physiological characteristics that correlate with the capacity to inhabit cooler (deeper, higher latitude) and even hypoxic waters. To achieve this goal, we discuss how these physiological traits are associated with habitat partitioning within the three-dimensional oceanic environment and with niche expansion into cooler and hypoxic waters. We also point out areas where additional research is needed to predict more accurately how future changes in oceanographic conditions will affect the distributions and movement patterns of tunas and their availability to fisheries.     

Separation of astaxanthin from cells of Phaffia rhodozyma using colloidal gas aphrons in a flotation column

The aim of this study is to investigate the separation of astaxanthin from the cells of Phaffia rhodozyma using colloidal gas aphrons (CGA), which are surfactant stabilized microbubbles, in a flotation column. It was reported in previous studies that optimum recoveries are achieved at conditions that favor electrostatic interactions. Therefore, in this study, CGA generated from the cationic surfactant hexadecyl trimethyl ammonium bromide (CTAB) were applied to suspensions of cells pretreated with NaOH. The different operation modes (batch or continuous) and the effect of volumetric ratio of CGA to feed, initial concentration of feed, operating height, and flow rate of CGA on the separation of astaxanthin were investigated. The volumetric ratio was found to have a significant effect on the separation of astaxanthin for both batch and continuous experiments. Additionally, the effect of homogenization of the cells on the purity of the recovered fractions was investigated, showing that the homogenization resulted in increased purity. Moreover, different concentrations of surfactant were used for the generation of CGA for the recovery of astaxanthin on batch mode; it was found that recoveries up to 98% could be achieved using CGA generated from a CTAB solution 0.8 mM, which is below the CTAB critical micellar concentration (CMC). These results offer important information for the scale‐up of the separation of astaxanthin from the cells of P. rhodozyma using CGA. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Mechanisms of sperm-egg interactions emerging from gene-manipulated animals

Sperm-egg interactions have been studied for many years using biochemical approaches such as the employment of antibodies and ligands that interact with sperm or with eggs and their vestments. As a result, various factors that participate in fertilization have emerged. However, when animals were genetically manipulated to examine the roles of those factors, most of them were found, to our surprise, to be "not essential". Of course, all biological systems contain redundancies and compensatory mechanisms, but at least some factors were found to be "essential" after gene disruption. As a whole, the explanations of sperm-egg interactions require significant modification from the gene manipulation point of view. In this review, information about sperm-egg interactions obtained from genetically manipulated animals is mainly revisited in order to propose a new vision.     

Predation on prokaryotes in the water column and its ecological implications

The oxic realms of freshwater and marine environments are zones of high prokaryotic mortality. Lysis by viruses and predation by ciliated and flagellated protists result in the consumption of microbial biomass at approximately the same rate as it is produced. Protist predation can favour or suppress particular bacterial species, and the successful microbial groups in the water column are those that survive this selective grazing pressure. In turn, aquatic bacteria have developed various antipredator strategies that range from simply 'outrunning' protists to the production of highly effective cytotoxins. This ancient predator-prey system can be regarded as an evolutionary precursor of many other interactions between prokaryotic and eukaryotic organisms.     

History of protein-protein interactions: from egg-white to complex networks

Today, it is widely appreciated that protein-protein interactions play a fundamental role in biological processes. This was not always the case. The study of protein interactions started slowly and evolved considerably, together with conceptual and technological progress in different areas of research through the late 19th and the 20th centuries. In this review, we present some of the key experiments that have introduced major conceptual advances in biochemistry and molecular biology, and review technological breakthroughs that have paved the way for today's systems-wide approaches to protein-protein interaction analysis.     

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS)     

Identification of hepatic copper-binding proteins from tilapia by column chromatography with proteomic approaches

Although copper is an essential element, it shows cytotoxic effects when present in excessive amounts with the production of hydroxyl radicals, which can damage phospholipids and enzymes. This necessitates a tight cellular control mechanism for copper homeostasis including its uptake and removal. The high copper contents in the liver of tilapia make this fish a suitable model for the study of copper binding proteins (CBPs). The liver was dissected from tilapia injected with Cu(2+) and cytosolic fractions were separated by using Superdex 75 column chromatography followed by atomic absorption spectrometry. Fractions in two major peaks containing CBPs were analyzed by using differential proteomic approaches, and loaded on a Cu chelating ion-immobilized affinity column (Cu-IMAC). Of the 113 differentially expressed proteins in these two peaks, 28 proteins were found to have copper binding ability, including well-characterized CBPs, such as copper transporter ATP7A and metallothionein. The networks of CBPs built up by Ingenuity Pathway Analysis (IPA) would help us to understand the transportation pathway and function of CBPs, which were related to free radical scavenging, cellular development and lipid metabolism. In addition, our results suggest that Cu(2+) would compete with Fe(2+) and Ca(2+) in binding with some target proteins, such as ferritin, transferrin, and calmodulin.     

Polymorphism of blood serum transcortin during column chromatography

Serum protein bound progestins, androgens, estrogens, and cortexolone, were fractionated on a number of chromatographic systems. Contrary to earlier suggestions of a homogeneous unit by competition binding and Scatchard analysis, polymorphism and heterogeneity in the molecular nature of the corticosteroid binding globulin (CBG) were evident with progesterone on Sephadex A-25 columns. Components in the 55 000 and 67 000 molecular weight regions were obtained with cortexolone, estradiol, progesterone and testosterone on Ultrogel columns. Separation on DEAE-cellulose-52 resin revealed a fraction in the low ionic prewash followed by another, highly charged entity eluted only with 0.06 M phosphate buffers. Thus, under these conditions, serum protein bound sex steroids eluted in the same position as transcortin glucocorticoid complexes. These results are presented as a caution against the universal use of association dissociation assays to study steroid ligand binding and biological response. The techniques here detailed may fruitfully be employed to explore the hydrodynamic characteristics of protein ligand interactions. In addition, they support the model, earlier proposed with tissue specific steroid receptors, that calls for the various subunits of the ligand as a prerequisite for the expression of all grades of agonist and antagonist activity of a given hormone.