Synthesis and properties of N-, O-, and S-phospho derivatives of amino acids, peptides, and proteins

The literature on chemical (i.e., nonenzymic) phosphorylation of amino acids, peptides, and proteins is reviewed through 1982. The review covers synthetic methods, chemical reactions, and physical properties, with emphasis on the techniques used for separation and characterization of the products. Synthetic methods are classified by reagent rather than product, and are illustrated by experimental procedures for the most important methods. Chemical reactions are classified into four groups depending on whether the reaction site is the phospho group, the amino group, the carboxyl group, or in the case of serine the hydroxyl group. Physical data are given for all of the known N-, O-, and S-phospho derivatives of the amino acids, peptides, and proteins, within certain limitations, and are discussed in detail in the section on physical properties. Emphasis is given to the techniques used for separation of the products, such as chromatography and electrophoresis, and for characterization of the products, particularly spectroscopy. Medical and other uses of the products are mentioned.     

Reverse engineering of metabolic networks, a critical assessment

Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.     

Preparation of vitamin K-dependent proteins,such as clotting factors II,VII, IX and X and clotting inhibitor protein C

A review is given of preparative methods for the isolation of the vitamin K-dependent clotting factors II, VII, IX, X and clotting inhibitor protein C, all derived from human plasma. Factor II, activated factor VII and activated protein C are also obtained from recombinant animal cells. The methods for their purification are described. The problem of difference in posttranslational modifications between plasma derived and recombinant protein is discussed with regard to therapeutic proteins.     

Dissection, Staining, and Mounting of the Embryos of Conifers

A statement is given of the advantages of this special technic and its place in embryological investigations, including directions for selecting the proper stages in collecting conifer cones and ovules, their methods of dissection from living material and their preservation for later dissection. The choice of dissecting microscopes and dissecting instruments, as well as directions for staining embryos with phloxine which may be combined with slow dehydration in glycerin, or for staining with Delafield's or Heidenhain's hematoxylin which may be followed by the glycerin dehydration are described. Glycerin affords a convenient break for a temporary stopping place in this technic.

Directions are given for transfer from glycerin thru 95% and absolute ethyl alcohol into other solvents such as diaphane solvent, essence of euparel or an easily prepared sandarac solvent. Other mounting media which have been used for conifer embryos are discussed—glycerin jelly, Venetian turpentine and Canada balsam—emphasizing the special advantages found in the media employing sandarac.     

Field-assisted extraction of cells, particles and macromolecules

Improved bioseparation techniques are increasingly important for biotechnology because separation is often the limiting factor for the success of biological processes. Manufacturers of new enzymes and pharmaceutical products require improved methods for recovering intact cells and intracellular products. Similarly the isolation, purification and concentration of many biomolecules produced in fermentation processes is extremely important. Often such downstream processing contributes a large portion of the product cost and thus efficient and economical alternative approaches to bioseparation processes are needed to eliminate, reduce or facilitate the handling of solids. Field-assisted separations, which hold immense potential for providing a major improvement in bioseparation in the near future, are considered in this review. Special emphasis is given to multistage methods, which are cost-effective compared with competing technologies. Commercial applications of these methods are detailed, we present suggestions for future work and we analyse the scale-up and economic aspects of these processes.     

Barriers to Sustained Use of Contraception in Nepal: Quality of Care,Socioeconomic Status,and Method-Related Factors

Owing to previously limited data availability, low contraceptive prevalence, and predominance of permanent method use in Nepal, there have been few studies of contraceptive-use dynamics. The aim of this article is to examine contraceptive use dynamics in Nepal in light of the country's ongoing fertility transition and change in contraceptive method-mix. Drawing on the 2003 Contraceptive Acceptance and Use Patterns Survey of Nepal and the quality-of-care framework, a proportional hazards model is used to explore contraceptive discontinuation of injections and pills. Results show that source of method from non-government services, high level of information given, one-to-one counseling, satisfaction with services, and shorter travel time to source are associated with lower odds of discontinuation. Despite the experience of side effects, women in Nepal are highly motivated to regulate their fertility. Results suggest detailed information given to users can have significant influence on continuation of methods rather than merely providing information on alternative methods and group counseling.     

Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants

The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor and TaqMan are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.     

Ecology of nematophagous fungi: Methods of collection,isolation and maintenance of predatory and endoparasitic fungi

The methods employed in a recent investigation into the ecology of nematophagous fungi are examined in detail. The best sources from which fungi can be isolated are examined, and the main field collection and recovery techniques are compared and discussed. Other practical problems considered are the examination of plates, microscopy, identification, isolation and culture methods, maintenance of fungi, the production of nematodes as bait. A summary of the experimental techniques used is given.     

Goals,methods and possibilities for directing development of limnic ecosystems

Case studies illustrating lake and wetland ecosystem problems as well as restoration methods are given. Among these methods, aeration of deep lakes, sediment removal from shallow, polluted lakes, sediment manipulation in polluted and acidified lakes, biomanipulation and wetland management methods are considered. A treatment program for directing ecosystem development is designed in each individual case according to lake type, degradation problems and goals of restoration. The most common goal in treatment of lakes is to meiotrophicate (oligotrophicate) hypertrophicated ecosystems. In the case of wetlands, conservation and restoration aspects are combined with a growing interest focused on biomass production by emergent macrophytes. Within practical frames of applied limnology, basic limnological research and training of doctorands have been organized as team-work for ecosystem-oriented investigations.     

Properties, Functions, and Secretion of Human Myeloperoxidase

The heme-containing protein myeloperoxidase is released from stimulated polymorphonuclear leukocytes at sites of inflammation. It is involved in the generation of reactive oxygen and nitrogen species and tissue damage. The general properties and functional aspects of this enzyme are reviewed. Special attention is given to luminescence methods for investigating the release of myeloperoxidase from stimulated cells.     

Estimation of zooplankton populations in Lake Maarsseveen I: Problems,procedures and results

During three successive years the zooplankton community of a small fresh water lake was sampled and counted weekly. A critical survey is given about the statistical methods employed in plankton research; much depends on sampling and subsampling strategies. It is shown that log-transformation is often unnecessary and that low densities can be estimated accurately with the aid of Poisson tables. For the analysis of time series, no straightforward mathematical instruments are available; spectral analysis has only limited value, so graphical methods are recommended. The results of the plankton counts are briefly discussed in relation to each other, temperature and phytoplankton biomass.     

The design, construction and use of a radio-tracking system for some British mammals

Radio-tracking equipment designed by the late G. E. Ashwell is described. Detailed instructions are given for building transmitters suitable for foxes and rats so that the circuits can be made by people with only limited electronic knowledge. Constructional details are also provided for receiver aerials. The address of a firm that can supply receivers is given. The function and performance of each part of the equipment is described and details provided of the methods used by the authors to track mammals. The handling of mammals and attachment of transmitters is covered briefly. Some comments are included on the limitations of radio-tracking as a means of studying wild mammals.     

Capture-recapture, epidemiology, and list mismatches: two lists

In recent years, capture-recapture methods for closed populations have been extensively applied to epidemiology. For example, suppose we have several incomplete lists of diabetics and we wish to estimate the total number of diabetics by estimating the number missing from all the lists. A major problem is that the information about individuals on the lists may have been given incorrectly or the information may have been typed incorrectly so that some list matches are missed. Using the concept of tag loss borrowed from animal population studies, we consider methods for estimating both the probabilities of making list errors and the population size for just two independent lists. The effect of heterogeneity on the errors is examined. The methods are applied to a large data set of diabetic persons consisting of a list obtained from a survey and a list obtained from doctors' records. It was found that the error rates were high and that ignoring the errors led to a gross overestimate of the total number of diabetic persons.     

Molecular recognition by gold, silver and copper nanoparticles

The intrinsic physical properties of the noble metal nanoparticles,which are highly sensitive to the nature of their local molecular environment,make such systems ideal for the detection of molecular recognition events.The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles.In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization.A brief discussion of the three common methods of functionalization:Electrostatic adsorption;Chemisorption;Affinity-based coordination is given.In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition.In the main section the various types of capping agents for molecular recognition;nucleic acid coatings,protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications.Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition.For the proteins the recognition properties of antibodies form the core of the section.With respect to the supramolecular systems the cyclodextrins,calix[n]arenes,dendrimers,crown ethers and the cucurbitales are treated in depth.Finally a short section deals with the possible toxicity of the nanoparticles,a concern in public health.     

Foaming: Consequences, prevention and destruction

This review examines the significance of foaming in bioprocesses, the mechanics of foam formation and destruction, and the methods of foam control and suppression. Emphasis is given to chemical antifoaming agents and characterization of their efficiencies. Criteria for selecting antifoaming agents are discussed.     

Ecology, metabolite production, and substrate utilization in endophytic fungi.

Endophytic fungi are a taxonomically and ecologically heterogenous group of organisms, mainly belonging to the Ascomycotina and Deuteromycotina. The isolation methods affect the species composition of the endophyte assemblage in a given host. The number of endophyte taxa isolated from a host species is usually large; however, only few, normally host specific species or strains are dominant. Endophyte assemblages are specific at the host species level, but species composition and frequencies are significantly affected by site-specific conditions. Moreover, the relative importance and number of endophytic species vary among individuals within sites. In some cases, each individual could be considered a separate ecosystem. In general, however, 40 individuals with 30 to 40 sampling units per organ and individual should be enough to detect 80% of taxa present in a given host at one site. Endophytes usually produce the enzymes necessary for the colonization of plant tissues. Substrate utilization studies and isozyme analysis have demonstrated that most endophytes are able to utilize most plant cell components. The production of growth promoting factors and of metabolites useful in the pharmaceutical and agricultural industry is widespread among endophytic fungi. The usefulness of endophytes in agricultural and pharmaceutical research is briefly discussed.     

Likelihood, parsimony, and heterogeneous evolution

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.     

Coherence, species turnover, and boundary clumping: elements of meta-community structure

Ecologists have identified several kinds of pattern in the distribution of species among sites, including a) nested subsets, b) checkerboards, c) Clementsian gradients, d) Gleasonian gradients, and e) evenly spaced gradients. Most past efforts to diagnose such patterns have focused on only one at a time, often contrasted with a sixth type of pattern, f) "randomness". While there are statistical tests to distinguish each of the first five patterns from randomness, there are currently no established methods for discriminating among these first five patterns in a given data set. Here we propose a method that will identify which of these possibilities is most prevalent in a site-by-species incidence matrix based on three basic aspects of meta-community structure. Our method is based on first ordinating the incidence matrix to identify the dominant axis of variation and identifying three aspects variation along this dominant axis. The first aspect, "coherence", is the degree to which pattern can be collapsed into a single dimension. The second, "species turnover", describes the number of species replacements along this dimension. The third aspect, "boundary clumping", has to do with how the edges of species boundaries are distributed along this dimension. We present methods for analyzing these three aspects of meta-community structure, use them to identify the six different patterns, and illustrate them with a representative set of cases drawn from previously published data.     

The effect of water temperature,current velocity and suspended solids on the distribution,growth and seasonality of Lemanea fluviatilis (C. Ag.), Rhodophyta,in the river Usk and other South Wales rivers

Two surveys of Lamanea in South Wales rivers have given details of its distribution, seasonality and range of tolerance to various environmental parameters, with particular reference to temperature, current velocity and suspended solids.Temperature, current velocity and suspended solids had most effect. Such findings were confirmed by principal component and correlation coefficient analysis.These investigations also suggest that abundant growths of Lemanea may be used in a limited manner as indicative of oligotrophic and metal free waters especially during Spring.In addition, transplants of Lemanea from the upper to the lower reaches of the River Usk and vice versa were studied to clarify the effect of suspended solids in nature.Using the ¹⁴C technique for primary production proved to be a successful method with Lamanea for comparison with chlorophyll a extraction and phycoerythrin. The importance of the latter in energy transfer for photosynthesis was revealed for this genus. A combination of various simple and cheap methods for the extraction of the pigment phycoerythrin was used successfully for the first time in red algal studies.Procedures for estimating percentage cover, standing crop and the presence/absence of the plant are given and the statistical reliability of the methods is evaluated.