Genotools SNP manager: a new software for automated high-throughput MALDI-TOF mass spectrometry SNP genotyping

Analysis of single nucleotide polymorphisms (SNPs) is a rapidly growing field of research that provides insights into the most common type of differences between individual genomes. The resulting information has a strong impact in the fields of pharmacogenomics, drug development, forensic medicine, and diagnostics of specific disease markers. The technique of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) has been shown to be a highly suitable tool for the analysis of DNA. It supplies a very versatile method for addressing a high-throughput SNP genotyping approach. Here, we present the Bruker genotools SNP MANAGER, a new software tool suitable for highly automated MALDI-TOF MS SNP genotyping. The genotools SNP MANAGER administers the sample preparation data, calculates masses of allele-specific primer extension products, performs genotyping analysis, and displays the results. In the current study, we have used the genotools SNP MANAGER to perform an automated duplex SNP analysis of two biallelic markers from the promoter of the gene encoding the inflammatory mediator interleukin-6.     

A DATA MANAGER for the health information system Berlin.

The needs for permanently changing the logical and physical structure of a medical datebase during the development of a health information system have initiated the project of implementing a DATA MANAGER. The concept of the DATA MANAGER covers facilities for the development of the logical data structure model including documentation of the model and programming support for application programs accessing the health information system (HIS) database. The outstanding facilities of the INTERLISP system have been found to be appropriate for writing the DATA MANAGER. A first data structure model, on which the DATA MANAGER will operate, is roughly outlined.     

Action of a thymic cytokine TsIF in reversing the autoimmune disease state of the MRL/1pr mouse

T suppressor cells differentiate from bone marrow precursors when cocultured with thymic epithelium, a thymic-derived cytokine TsIF, or mixture of both. (TsIF is a trademark of Ventrex Laboratories, Inc., Portland, ME, and is the subject of a U.S. patent by Ventrex Laboratories, Inc., Portland, ME.) These cells, when transplanted into the lupus-rheumatoid arthritis-prone mouse, prevent acquisition of disease as assessed by lack of both antinuclear antibody, rheumatoid factor, and survival beyond mean time for MRL/lpr mice. When TsIF is administered directly into these lupus-rheumatoid arthritis-prone mice, an equivalent sparing effect is manifested.     

Disease mapping in veterinary parasitology: an update

The development of methods for disease mapping has progressed considerably in recent years. Geographical Information Systems (GIS) and Remote Sensing (RS) represent new tools for the study of epidemiology, and their application to veterinary medicine, and in particular to veterinary parasitology, has become more and more advanced to study the spatial and temporal patterns of diseases. The present paper reports an update regarding the use of these technologies in veterinary parasitology.     

PhyloGeoViz: a web-based program that visualizes genetic data on maps

The first step of many population genetic studies is the simple visualization of allele frequencies on a landscape. This basic data exploration can be challenging without proprietary software, and the manual plotting of data is cumbersome and unfeasible at large sample sizes. I present an open source, web-based program that plots any kind of frequency or count data as pie charts in Google Maps (Google Inc., Mountain View, CA). Pie polygons are then exportable to Google Earth (Google Inc.), a free Geographic Information Systems platform. Import of genetic data into Google Earth allows phylogeographers access to a wealth of spatial information layers integral to forming hypotheses and understanding patterns in the data.     

An integrated comparative approach to mangrove vegetation mapping using advanced remote sensing and GIS technologies: preliminary results

This study aims to develop an integrated methodology applying Remote Sensing and Geographic Information Systems (GIS) techniques for the assessment of the ecological status of mangrove forests. The study area is located at Phangnga Bay, Thailand. Various commonly available remote sensing data are evaluated for mangrove vegetation mapping. The satellite sensors used are covering the visible and infra-red (VIR) spectrum up to the microwave region of the electromagnetic spectrum. This study provides recommendations regarding the selection of a single sensor approach or sensor combination that fulfills a minimum requirement for practical mangrove mapping and inventory purposes (e.g. mangrove and non-mangrove areas, varying stocking density, dominant species composition and impact of human activities). Both their technical capabilities and their potentials are presented in correlation with the existing ground conditions.Asian Institute of Technology Bangkok, Thailand; National Research Council of Thailand Bangkok, Thailand; Royal Forestry Department Bangkok, Thailand     

Study of age dependent half-life of iodine in man: A reinforcement-depletion urn model

An urn contains balls ofs different colors. The problem of the reinforcement of a specified color and random depletion of balls has been considered by Shenton (1981, 1983). In this paper, the theory is applied to the biological age dependent half-life of radioactive iodine in man; the data of Cook and Snyder (1965) is used. The intake of radioactive iodine and its retention subsequently is studied. Research sponsored by the Office of Health and Environmental Research, Office of Energy Research, U.S. Department of Energy under contract DE-AC05-840R21400 with the Martin Merietta Energy Systems. Inc.     

Precision Farming and Precision Pest Management: The Power of New Crop Production Technologies

The use of new technologies including Geographic Information Systems (GIS), the Global Positioning System (GPS), Variable Rate Technology (VRT), and Remote Sensing (RS) is gaining acceptance in the present high-technology, precision agricultural industry. GIS provides the ability to link multiple data values for the same geo-referenced location, and provides the user with a graphical visualization of such data. When GIS is coupled with GPS and RS, management decisions can be applied in a more precise "micro-managed" manner by using VRT techniques. Such technology holds the potential to reduce agricultural crop production costs as well as crop and environmental damage.     

Human teratogens: update 2010

A wide variety of human teratogens have been identified. The characteristics of human teratogens can be used in the assessment of apparent “new” teratogens, when postulated. Information is available through online databases, such as TERIS and Reprotox, telephone‐based counseling resources (e.g., Organization of Teratogen Information Systems [OTIS] and European Network Teratology Information Services [ENTIS]), reference books, annual meetings of the Teratology Society, and published articles. There are significant deficiencies in the information available: (1) lack of knowledge about the molecular and cellular basis for most teratogenic effects; (2) the inability to genetically identify more susceptible women before pregnancy; (3) little information is available on dermal and airborne exposures during pregnancy; and (4) most clinicians receive little, if any, training in the identification of or counseling for exposure to potential teratogens. There are many current dilemmas in counseling about exposures in pregnancy, including: (1) Is exposure to specific drugs, such as selected serotonin re‐uptake inhibitors (SSRIs) and the inhibitors of tumor necrosis factor‐alpha, teratogenic in the first trimester of pregnancy? (2) Are the increased risks of birth defects associated with assisted reproductive technology due, in part, to epigenetic effects? (3) What are the “safe” levels of exposure to the plasticizers phthalates during pregnancy? (4) How do we convince busy physicians, nurses, and pharmacists not to use the drug categories A, B, C, D, and X in counseling and to use more accurate sources? There is a need for a national advisory center for pregnancy registries to provide guidance when new registries are being developed. Birth Defects Research (Part A), 2011. © 2011 Wiley‐Liss, Inc.     

Molecular Probe Data Base (MPDB).

This paper provides an update on the contents and structure, forms and mode of data distribution of the Molecular Probe Data Base (MPDB), a database that collects and provides on-line information on the sequence, target gene, applications and bibliographic references of synthetic oligonucleotides. The recent data extension and the new means of accessing the database are discussed.     

Steady state terrestrial ecosystems and the global carbon cycle

The assumption that landscapes dominated by mature vegetation are presently in carbon steady state with the atmosphere is challenged. Evidence suggests that the vegetation and soils of these landscapes are frequently disturbed and over short time periods (<300 yr) slowly sequester atmospheric carbon. The critical consideration in this argument is the time interval used to evaluate a steady state. Current models of carbon flux through the terrestrial biota limit their time considerations to 120 yr, a short and inadequate time interval for realistic assumptions about steady state in the carbon cycle of vegetation.Research performed under subcontract 19B-07762C with S. Brown and 19X-43326C with the Center for Energy and Environment Research of the University of Puerto Rico (A. E. Lugo) under Martin Marietta Energy Systems, Inc., contract DE-AC05-840R21400 with the U.S. Department of Energy.     

Threshold Conditions for West Nile Virus Outbreaks

In this paper, we study the stability and saddle-node bifurcation of a model for the West Nile virus transmission dynamics. The existence and classification of the equilibria are presented. By the theory of K-competitive dynamical systems and index theory of dynamical systems on a surface, sufficient and necessary conditions for local stability of equilibria are obtained. We also study the saddle-node bifurcation of the system. Explicit subthreshold conditions in terms of parameters are obtained beyond the basic reproduction number which provides further guidelines for accessing control of the spread of the West Nile virus. Our results suggest that the basic reproductive number itself is not enough to describe whether West Nile virus will prevail or not and suggest that we should pay more attention to the initial state of West Nile virus. The results also partially explained the mechanism of the recurrence of the small scale endemic of the virus in North America. Supported by the Chinese NSF grants 10531030 and 10671143. Supported by the Chinese NSF grants 10801074. Supported by Canada Research Chairs Program, Mathematics for Information Technology and Complex Systems (MITACS), National Microbiology Laboratory, Natural Sciences and Engineering Research Council (NSERC), Canadian Foundation of Innovation (CFI) and Ontario Innovation Trust (OIT), Ontario Ministry of Health and Long-term Care, Peel, Toronto, Chat-Kent Health Units, and Public Health Agency of Canada (PHAC). Supported by NSERC, MITACS, CFI/OIT a new opportunity fund, Early Research Award of Ministry of Research and Innovation (ERA) of Ontario, Infectious Diseases Branch of Ministry of Health and Long Term Care (MOH) of Ontario and PHAC.     

Optimal HIV treatment by maximising immune response

We present an optimal control model of drug treatment of the human immunodeficiency virus (HIV). Our model is based upon ordinary differential equations that describe the interaction between HIV and the specific immune response as measured by levels of natural killer cells. We establish stability results for the model. We approach the treatment problem by posing it as an optimal control problem in which we maximise the benefit based on levels of healthy CD4+ T cells and immune response cells, less the systemic cost of chemotherapy. We completely characterise the optimal control and compute a numerical solution of the optimality system via analytic continuation.Research supported by the Natural Science and Engineering Research Council (NSERC) and the Mathematics of Information Technology and Complex Systems (MITACS) of Canada     

Funding for teratology information services: Up, down, and all around

Funding for Teratology Information Services has been an ongoing struggle over the 25 years of its existence. Traditional and novel funding mechanisms have been explored with varying success. The importance of providing teratology risk assessment and counseling to all women of reproductive age is now an established health care objective. Sufficient and stable funding for these services is essential. Birth Defects Research (Part A) 94:660-663, 2012. ? 2012 Wiley Periodicals, Inc.     

Development of chiral drugs in Japan: An update on regulatory and industrial opinion

The purpose of this commentary is to provide information on the present status of the racemate/enantiomer debate in Japan and current industrial and regulatory attitudes to chiral drugs in Japan. It provides an update of our previous paper (Shindo and Caldwell, Chirality 3:91–93, 1991), and the interested reader is referred to this for background information. © 1995 Wiley-Liss, Inc.     

Comparative genotoxicity testing of mainstream whole smoke from cigarettes which burn or heat tobacco

The genotoxic potential of mainstream whole smoke (MWS) from cigarettes which heat tobacco (TEST) was compared to the genotoxic potential of MWS from a cigarette which burns tobacco (REFERENCE). MWS was collected from a University of Kentucky 1R4F cigarette (REFERENCE) and two, TEST cigarettes, one with regular flavor and the other with menthol flavor. All cigarettes were smoked on a smoking machine and the particulate phase was collected on Cambridge filter pads. The vapor phase, which passed through the pad, was bubbled into a dimethyl sulfoxide (DMSO) trap. The filter pad was extracted with the DMSO in the trap and additional DMSO to obtain MWS. MWS representing an identical number of cigarettes was tested to make a per-cigarette comparison of their genotoxic potential. REFERENCE MWS was mutagenic and cytotoxic in the Ames assay in the presence of metabolic activation while it was cytotoxic but not mutagenic in the absence of metabolic activation. Statistically significant increases in frequency of both sister-chromatid exchanges and chromosomal aberrations were observed in Chinese hamster ovary cells exposed to REFERENCE MWS with and without metabolic activation. MWS from the TEST cigarettes, with either regular or menthol flavor, was neither cytotoxic nor mutagenic in any of these assays. In summary, MWS from the 2 TEST cigarettes was neither genotoxic nor cytotoxic under conditions where MWS from the REFERENCE cigarettes was genotoxic and/or cytotoxic in a concentration-dependent manner.     

Critical delay for overshooting in planned arm movements with delayed feedback

The Vector Integration To Endpoint (VITE) circuit describes a real time neural network model which simulates behavioral and neurobiological properties of planned arm movements by the interaction of two populations of neurons. This model is generalized to include delay between the interacting populations, which is found to have a detrimental effect on movement accuracy. Conditions are given on the model parameters for accurate movement and target overshoot, where we show that there exists a non-zero critical value of the delay which the circuit can support while maintaining accurate movement. This critical delay depends on the movement speed, and becomes arbitrarily large for sufficiently slow movement. Thus neurobiological or artificial systems modelled by the VITE sensory-motor loop can tolerate an arbitrarily large delay if the movement speed is sufficiently slow.Acknowledgement This project was partially supported by Mathematics for Information Technology and Complex Systems, by the Canada Research Chairs program, and by the Natural Science and Engineering Research Council of Canada.     

Sustained degradation of n-pentane and isobutane in a gas-phase bioreactor

Summary Microorganisms were able to remove hydrocarbons (pentane and isobutane) from air by biological action in a columnar bioreactor with ceramic packing. The reactor was operated in a liquid continuous mode with gas recirculation and a slow addition of the organic-containing air. After a period of acclimation, the reactor has operated for 12 months with only pentane and isobutane as carbon sources. The gaseous hydrocarbons have been degraded throughout this period. The hydrocarbon removal rates measured between 1 and 2 g h^–1 m^–3. The microbes were shown to be able to degrade these gaseous hydrocarbons completely in a closed bioreactor without any additional nutrients.Research supported by the Advanced Industrial Concepts Division-Biological and Chemical Technologies Research. U.S. Department of Energy, under contract DE-AC05-84OR21400 with Martin Marietta Energy Systems. Inc.     

Selecting, testing and understanding probiotic microorganisms

The interest in probiotics and the modulation of microbiota for restoring and maintaining health continues to gain momentum. Research is fueled by a need to develop alternatives to antibiotics and drugs that have severe side effects. It is recognised that bacteria play a major role in human and animal health, and how scientific advances help to explain how and when probiotics work. This minireview provides an update on critical studies, particularly since 2002, that are helping to explain the mechanisms of action of probiotic organisms.