Mushrooms, tumors, and immunity.

Medicinal properties have been attributed to mushrooms for thousands of years. Mushroom extracts are widely sold as nutritional supplements and touted as beneficial for health. Yet, there has not been a critical review attempting to integrate their nutraceutical potential with basic science. Relatively few studies are available on the biologic effects of mushroom consumption, and those have been performed exclusively in murine models. In this paper, we review existing data on the mechanism of whole mushrooms and isolated mushroom compounds, in particular (1-->3)-beta-D-glucans, and the means by which they modulate the immune system and potentially exert tumor-inhibitory effects. We believe that the antitumor mechanisms of several species of whole mushrooms as well as of polysaccharides isolated from Lentinus edodes, Schizophyllum commune, Grifola frondosa, and Sclerotinia sclerotiorum are mediated largely by T cells and macrophages. Despite the structural and functional similarities of these glucans, they differ in their effectiveness against specific tumors and in their ability to elicit various cellular responses, particularly cytokine expression and production. Unfortunately, our data base on the involvement of these important mediators is still rather limited, as are studies concerning the molecular mechanisms of the interactions of glucans with their target cells. As long as it remains unclear what receptors are involved in, and what downstream events are triggered by, the binding of these glucans to their target cells, it will be difficult to make further progress in understanding not only their antitumor mechanisms but also their other biological activities.     

The glutathione system. II. Other enzymes, thiol-disulfide metabolism, inflammation, and immunity, functions

The great importance of glutathione as a redox regulator and the reducing carrier has been recognized. There is clear necessity for subdivision of an independent mitochondrial glutathione subsystem. The data on specific features of glutathione metabolism in different organs are accumulated. There is convincing evidence for the involvement of the glutathione system into inflammation and immunity. Studies of the glutathione system are used in medicine for elucidation of pathogenesis of diseases and their diagnostics.     

Human adenine phosphoribosyltransferase. Affinity purification, subunit structure, amino acid composition, and peptide mapping.

Adenine phosphoribosyltransferase (EC 2.4.2.7) has been purified 55,000-fold from normal human erythrocytes. The native molecular weight of the enzyme is 38,200 as determined by sedimentation equilibrium centrifugation. The subunit molecular weight is 18,000 as determined by sodium dodecyl sulfate gel electrophoresis and 17,000 as determined by gel filtration in guanidine hydrochloride, suggesting that the enzyme is a dimer in its native state. Cross-linking the enzyme with dimethylsuberimidate confirms the dimeric structure and peptide mapping data suggested that the subunits are quite similar if not identical. The amino acid composition reveals that 33% of the residues are hydrophobic.     

Introducing W.A.T.E.R.S.: a Workflow for the Alignment,Taxonomy, and Ecology of Ribosomal Sequences

Background  

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.     

Noise, sensitivity, and resolution of flow cytometers.

The sensitivity and resolution of flow cytometers are functions of the signal produced by a given particle as well as by the noise in the presence of which the signal is detected. The noise is primarily due to the fact that emission of light as well as its detection by photoelectric devises are stochastic processes. This fact leads to equations describing how resolution and sensitivity are limited by the magnitude of the signal, the background, and the photoelectron quantum yield of the detector. The equations are pointing to a method by which the signal and noise of a flow cytometer can be measured in absolute terms, as well as a way to determine fluorescence sensitivity without having to extrapolate to the noise level. The equations appear to be validated when applied to measuring data obtained with two different flow cytometers.     

The genetic structure of a tribal population,the Yanomama Indians. XII. Biodemographic studies

The Yanomama Indians of Southern Vanezuela and Northern Brazil are one of the largest, relatively unacculturated tribes of the tropical rain forest. Over a period of eight years data have been collected from a considerable portion of their territory on estimated age, sex ratio, fertility rates (as determined by physical examination and urine tests), and infant death rates. Although it has been impossible to collect direct data on infanticide, this subject can be approached indirectly through distortions of the sex ratio and anecdotal information. Some historical data are also available as a basis for estimating tribal expansion in the past 100 years. With this material it has been possible to construct Life Tables for the Yanomama, and to explore the results of various perturbations of the input parameters. Data are also presented on patterns of mating and reproduction: number of spouses, mean and variance in number of surviving children, frequency of “extra-marital conceptions” based on the results of extensive blood group typings, and consanguinity rates as determined by observation and computer simulation. Although we do not present the Yanomama as typical, these data are seen as providing a basis for more realistic population models than have existed in the past. In addition, the data provide a basis for relatively precise estimates of such demographic measures as Fisher's Reproductive Value, Crow's Index of Total Selection, and Weiss' Index of Growth Regulation.     

On-line measurement in biotechnology: exploitation, objectives and benefits.

Sound data biologically relevant are prerequisites when developing high-performance bioprocesses. Understanding of physiological regulation as well as sophisticated control strategies are highly dependent on the observability of the culture, i.e. the generation and exploitation of suited signals even under complex environmental measurement conditions. Against this background, the increasing number of analytical systems is very supportive and, accordingly, an appropriate handling of sensors and measured data is of decisive importance. This article reports on practical experience with routines for maintenance, service and calibration of hardware sensors which improve the quality of measurements significantly. Verification and validation of signals is outlined in order to make the value of data exploitation tools obvious. A method for the characterization of information is introduced by practical examples of Saccharomyces cerevisiae cultures when explaining the specific properties of extracting biological information from raw data. Finally, examples for advantageous exploitation of on-line data are given.     

Evaluation of numerical analyses of RAPD and API 50 CH patterns to differentiate Lactobacillus plantarum, Lact. fermentum, Lact. rhamnosus, Lact. sake, Lact. parabuchneri, Lact. gallinarum, Lact. casei, Weissella minor and related taxa isolated from kocho and tef

AIM: The study was carried out to assess the agreement of API 50 CH fermentation data of food lactobacilli with their RAPD profiles to determine whether the system could be used alone as a reliable taxonomic tool for this genus. METHODS AND RESULTS: API 50 CH, RAPD and DNA:DNA reassociation data for 42 lactobacilli from tef and kocho were compared with 30 type strains. Discrepancies were observed between the three methods in assigning strains of Lactobacillus plantarum, Lact. fermentum, Weissella minor and Lact. gallinarum, and Lact. fermentum, Lact. amylophilus, Lact. casei subsp. pseudoplantarum and Lact. rhamnosus. DNA reassociation data agreed well with RAPD results. CONCLUSIONS: API 50 CH profiles should be complemented with molecular genetic results for effective identification in Lactobacillus. SIGNIFICANCE AND IMPACT OF THE STUDY: The study suggested less dependability of metabolic data alone as an identification tool.     

Resources, standards and tools for systems biology.

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation. In this review, we describe different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology.     

The Homeodomain Resource: sequences, structures and genomic information.

The Homeodomain Resource is a comprehensive collection of sequence, structure and genomic information on the homeodomain protein family. Available through the Resource are both full-length and domain-only sequence data, as well as X-ray and NMR structural data for proteins and protein-DNA complexes. Also available is information on human genetic diseases and disorders in which proteins from the homeodomain family play an important role; genomic information includes relevant gene symbols, cytogenetic map locations, and specific mutation data. Search engines are provided to allow users to easily query the component databases and assemble specialized data sets. The Homeodomain Resource is available through the World Wide Web at http://genome.nhgri.nih.gov/homeodomain     

Stream Restoration in the Upper Midwest, U.S.A.

Restoration activities intended to improve the condition of streams and rivers are widespread throughout the Upper Midwest, U.S.A. As with other regions, however, little information exists regarding types of activities and their effectiveness. We developed a database of 1,345 stream restoration projects implemented from the years 1970 to 2004 for the states of Michigan, Ohio, and Wisconsin in order to analyze regional trends in goals, presence of monitoring, spatial distribution, size, and cost of river restoration projects. We found that data on individual projects were fragmented across multiple federal, state, and county agencies, as well as nonprofit groups and consulting firms. The most common restoration goals reported for this region were in‐stream habitat improvement, bank stabilization, water‐quality management, and dam removal. The former two were most common in Michigan and Wisconsin, where salmonid fisheries enhancement appeared to be an important concern, whereas water‐quality management was most frequent in Ohio. The most common restoration activities were the use of sand traps and riprap, and other common activities were related to the improvement of fish habitat. The median cost was $12,957 for projects with cost data, and total expenditures since 1990 were estimated at $444 million. Over time, the cost of individual projects has increased, whereas the median size has decreased, suggesting that restoration resources are being spent on smaller, more localized, and more expensive projects. Only 11% of data records indicated that monitoring was performed, and more expensive projects were more likely to be monitored. Standardization of monitoring and record keeping and dissemination of findings are urgently needed to ensure that dollars are well spent and restoration effectiveness is maximized.     

Twins, chorionicity and zygosity.

Accurate determination of zygosity and chorionicity is essential in all multiple maternities. The parents and the multiples themselves ask it. It is of medical importance and now considered as a prerequisite in several domains of twin research, especially when perinatal data are analysed. It helps the multiples and their parents and teachers to ascertain identity. The methods are briefly described and a plea is made to obstetricians and paediatricians to use them systematically at the time of birth.     

GEL, a DNA sequencing project management system.

We have developed an automated system for management of DNA sequencing projects. The system, named GEL, can handle data from both random sequences and from fragments whose relative positions are known. The system is highly interactive, self-documenting, and forgiving; it is designed for use by computer-naive molecular biologists. An editor designed specifically for sequences allows simple entry of data. Special functions allow direct checking and immediate editing of paired readings of the same gel. Merging of new random fragment sequences into the project as a whole is semi-automated. The user is shown probable overlaps if they exist, and can edit either the sequences or the consensus. Heuristic approaches to limiting the kinds of searches made in the merging process reduces the problem of combinatoric data overload as sequencing projects grow large. Complete histories of all entries, editing changes, and generation of consensus sequences are automatically prepared.     

DNA analysis servers: plot.it,bend.it,model.it and IS

The WWW servers at http://www.icgeb.trieste.it/dna/ are dedicated to the analysis of user-submitted DNA sequences; plot.it creates parametric plots of 45 physicochemical, as well as statistical, parameters; bend.it calculates DNA curvature according to various methods. Both programs provide 1D as well as 2D plots that allow localisation of peculiar segments within the query. The server model.it creates 3D models of canonical or bent DNA starting from sequence data and presents the results in the form of a standard PDB file, directly viewable on the user's PC using any molecule manipulation program. The recently established introns server allows statistical evaluation of introns in various taxonomic groups and the comparison of taxonomic groups in terms of length, base composition, intron type etc. The options include the analysis of splice sites and a probability test for exon-shuffling.     

Synthesis of a hormonally active conjugate of alpha-MSH, ferritin, and fluorescein.

A flow assay device for the study of steady-state enzyme kinetics is described. The apparatus employs a peristaltic pump and has a fluorimeter as the monitoring device. An automatic data storage and handling system is used. Theoretical considerations are made on the determination of the apparent initial velocity and flow-induced distortion of the initial velocity versus initial substrate concentration profile. Several analytical expressions useful in calculating the magnitudes of errors and for designing experiments are given. The distortion of output evident in this and in a previously described apparatus of a similar kind is removed by use of Fourier deconvolution using the response of the instrument to a δ function input. Some data obtained with rabbit muscle glyceraldehyde-3-phosphate dehydrogenase, which displays nonhyperbolic kinetics, are discussed and used as an illustration of the application of the method.     

Cryptococcus tephrensis,sp.nov., and Cryptococcus heimaeyensis,sp.nov.; new anamorphic basidiomycetous yeast species from Iceland

Two new species from Iceland are described on the basis of physiological profiles and sequence data from the D2 region of LSU rDNA: Cryptococcus tephrensis (type ICE99-IToM Y5, ATCC MYA-1765, CBS 8935, GenBank AF317208) and Cryptococcus heimaeyensis (type ICE99-IToM Y8, ATCC MYA-1759, CBS 8933, GenBank AF370717). The two new species are identifiable from sequence data and can be distinguished from their closest relative, Cryptococcus victoriae, by their higher maximum temperatures for growth, failure to utilize nitrate as sole nitrogen source, and utilization of cadaverine and ethylamine as sole nitrogen sources. Cryptococcus tephrensis is distinguishable from C. heimaeyensis by failure to grow on saccharate as sole source of carbon and energy.     

Bioinformatics and Computational Biology Solutions Using R and Bioconductor. * Edited by Robert Gentleman, Wolfgang Huber, Vincent J. Carey, Rafael A. Irizarry and Sandrine Dudoit

This book guides through practical bioinformatics data analysisusing the Bioconductor toolkit, which is based on the statisticallanguage R. R itself is an open-source recreation of the languageS-Plus. The Bioconductor is a collection of R-packages for theanalysis of genomic and molecular biological data generatedin high-throughput experiments. High-throughput experimentsare characterized by large amounts of data generated in shortperiods of time on a sizable number of samples. This poses newchallenges to the analysis such as assessing and adjusting fornoise, exploration using cluster-analysis, visualization, andlinking to (or ‘annotating with’) biomedical knowledgebases. The book focuses on gene expression microarrays, the high-throughputtechnology for which statistical methods are best developedtoday. In addition, a