BSD: the Biodegradative Strain Database

The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The BSD (http://bsd.cme.msu.edu) is being developed within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.msu.edu/html) to provide a biological complement to the chemical and degradative pathway data of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD: http://umbbd.ahc.umn.edu). Data is accessible through a series of strain, chemical and reference lists or by keyword search. The web site also includes on-line data submission and user survey forms to solicit user contributions and suggestions. The current release contains information on over 250 degradative bacterial strains and 150 hazardous substances. The transformation of xenobiotics and other environmentally toxic compounds by microorganisms is central to strategies for biocatalysis and the bioremediation of contaminated environments. However, practical, comprehensive, strain-level information on biocatalytic/biodegradative microbes is not readily available and is often difficult to compile. Similarly, for any given environmental contaminant, there is no single resource that can provide comparative information on the array of identified microbes capable of degrading the chemical. A web site that consolidates and cross-references strain, chemical and reference data related to biocatalysis, biotransformation, biodegradation and bioremediation would be an invaluable tool for academic and industrial researchers and environmental engineers.     

Role of bradykinin in angiotensin-converting enzyme knockout mice

Angiotensin-converting enzyme (ACE) plays a central role in the renin-angiotensin system. Whereas ACE is responsible for the production of angiotensin II, it is also important in the elimination of bradykinin. Constitutively, the biological function of bradykinin is mediated through the bradykinin B(2) receptor. ACE knockout mice have a complicated phenotype including very low blood pressure. To investigate the role of bradykinin in the expression of the ACE knockout phenotype, we bred B(2) receptor knockout mice with ACE knockout mice, thus generating a line of mice deficient in both the B(2) receptor and ACE. Surprisingly, these mice did not differ from ACE knockout mice in blood pressure, urine concentrating ability, renal pathology, and hematocrit. Thus abnormalities of bradykinin accumulation do not play an important role in the ACE knockout phenotype. Rather, this phenotype appears due to the defective production of angiotensin II.     

Relationship of tadpole stage to location of echinostome cercariae encystment and the consequences for tadpole survival

The effect of echinostome infections on the survival of Rana pipiens tadpoles was examined in relation to developmental stage of tadpoles. Individual tadpoles of Gosner stages 25, 27, 32-33, and 37-39 were exposed to 1 of 4 levels of cercariae (0, 20, 50, or 100). Only tadpoles at stage 25, the earliest stage infected, died within a 5-day experimental period. This stage-specific mortality rate could be explained, in part, by the stage-specific location of encystment of cercariae, which was documented in a separate experiment. In accordance with kidney development, cercariae predominately encysted in the pronephroi during early stages of tadpole development (stages 25 through 31-32) and only in the mesonephroi and associated ducts at later stages (stages 37 through 46). As the mesonephros develops, renal capacity presumably increases. Thus, tadpoles died only when metacercariae concentrated in the functional portion of the kidney with the most limited renal capacity. As tadpoles aged, they also became less susceptible to infections. On average, 69.5% of cercariae that were exposed to stage 25-26 tadpoles successfully encysted. compared with only 8.4% of cercariae exposed to stage 37-38 tadpoles. Exposures of metamorphic frogs (poststage 46) to cercariae revealed that these individuals can become infected with echinostomes. Collectively, our data highlight the host stage-dependent dynamics of tadpole-echinostome interactions.     

Immunization of newborn rhesus macaques with simian immunodeficiency virus (SIV) vaccines prolongs survival after oral challenge with virulent SIVmac251

There is an urgent need for active immunization strategies that, if administered shortly after birth, could protect infants in developing countries from acquiring human immunodeficiency virus (HIV) infection through breast-feeding. Better knowledge of the immunogenic properties of vaccine candidates in infants and of the effect of maternal antibodies on vaccine efficacy will aid in the development of such a neonatal HIV vaccine. Simian immunodeficiency virus (SIV) infection of infant macaques is a useful animal model of pediatric HIV infection with which to address these questions. Groups of infant macaques were immunized at birth and 3 weeks of age with either modified vaccinia virus Ankara (MVA) expressing SIV Gag, Pol, and Env (MVA-SIVgpe) or live-attenuated SIVmac1A11. One MVA-SIVgpe-immunized group had maternally derived anti-SIV antibodies prior to immunization. Animals were challenged orally at 4 weeks of age with a genetically heterogeneous stock of virulent SIVmac251. Although all animals became infected, the immunized animals mounted better antiviral antibody responses, controlled virus levels more effectively, and had a longer disease-free survival than the unvaccinated infected monkeys. Maternal antibodies did not significantly reduce the efficacy of the MVA-SIVgpe vaccine. In conclusion, although the tested vaccines delayed the onset of AIDS, further studies are warranted to determine whether a vaccine that elicits stronger early immune responses at the time of virus exposure may be able to prevent viral infection or AIDS in infants.     

A new method for quantifying encephalization in the growing individual

Here we describe a new method for quantifying encephalization in the growing individual and provide a worked example of the methods. The new method is based on the use of conditional SD scores derived from brain and body growth references. These encephalization SD scores control for age, sex and body size effects on brain size, and therefore, control for the confounds associated with allometry as well as growth differences between the brain and body and between the sexes. The methods also control for distribution skewness. Encephalization SD scores derived from pre- and post-natal data may be directly compared and changes in SD score over time assessed. These methods may be applied to a broad range of data where relative size during growth is to be quantified. Derived SD scores may also be applied to correlation and regression analyses where statistical relationships with other variables are of interest.     

COX-2 induction during murine gammaherpesvirus 68 infection leads to enhancement of viral gene expression

The murine gammaherpesvirus 68 (MHV-68 or gammaHV-68) model provides many advantages for studying virus-host interactions involved in gammaherpesvirus replication, including the role of cellular responses to infection. We examined the effects of cellular cyclooxygenase-2 (COX-2) and its by-product prostaglandin E(2) (PGE(2)) on MHV-68 gene expression and protein production following de novo infection of cultured cells. Western blot analyses revealed an induction of COX-2 protein in MHV-68-infected cells but not in cells infected with UV-irradiated MHV-68. Luciferase reporter assays demonstrated activation of the COX-2 promoter during MHV-68 replication. Two nonsteroidal anti-inflammatory drugs, a COX-2-specific inhibitor (NS-398) and a COX-1-COX-2 inhibitor (indomethacin), substantially reduced MHV-68 protein production in infected cells. Inhibition of viral protein expression and virion production by NS-398 was reversed in the presence of exogenous PGE(2). Global gene expression analysis using an MHV-68 DNA array showed that PGE(2) increased production of multiple viral gene products, and NS-398 inhibited production of many of the same genes. These studies suggest that COX-2 activity and PGE(2) production may play significant roles during MHV-68 de novo infection.     

Evaluation of F+ RNA and DNA coliphages as source-specific indicators of fecal contamination in surface waters

Male-specific (F+) coliphages have been investigated as viral indicators of fecal contamination that may provide source-specific information for impacted environmental waters. This study examined the presence and proportions of the different subgroups of F+ coliphages in a variety of fecal wastes and surface waters with well-defined potential waste impacts. Municipal wastewater samples had high proportions of F+ DNA and group II and III F+ RNA coliphages. Bovine wastewaters also contained a high proportion of F+ DNA coliphages, but group I and IV F+ RNA coliphages predominated. Swine wastewaters contained approximately equal proportions of F+ DNA and RNA coliphages, and group I and III F+ RNA coliphages were most common. Waterfowl (gull and goose) feces contained almost exclusively F+ RNA coliphages of groups I and IV. No F+ coliphages were isolated from the feces of the other species examined. F+ coliphage recovery from surface waters was influenced by precipitation events and animal or human land use. There were no significant differences in coliphage density among land use categories. Significant seasonal variation was observed in the proportions of F+ DNA and RNA coliphages. Group I F+ RNA coliphages were the vast majority (90%) of those recovered from surface waters. The percentage of group I F+ RNA coliphages detected was greatest at background sites, and the percentage of group II F+ RNA coliphages was highest at human-impacted sites. Monitoring of F+ coliphage groups can indicate the presence and major sources of microbial inputs to surface waters, but environmental effects on the relative occurrence of different groups need to be considered.     

Cloning,characterization and regulation of a family of phi class glutathione transferases from wheat

Six phi (F) class glutathione transferases (GSTs) were cloned from bread wheat (Triticum aestivum L.) treated with the herbicide safener fenchlorazole ethyl and named TaGSTF1–6. Recombinant TaGSTFs were assayed for glutathione conjugating activity towards xenobiotics including herbicides and for glutathione peroxidase (GPOX) activity. TaGSTF1, which resembled ZmGSTF1, the dominant GST in maize (Zea mays), was highly active in conjugating 1-chloro-2,4-dinitrobenezene (CDNB) but had low activities towards chloroacetanilide, diphenyl ether and aryloxphenoxypropionate herbicides. TaGSTF2, TaGSTF3 and TaGSTF4 all resembled the safener-inducible ZmGSTF2, with TaGSTF2 and TaGSTF3 being highly active GPOXs and rapidly detoxifying chloroacetanilides. TaGSTF5 resembled ZmGSTF3, having limited conjugating and GPOX activity. TaGSTF6 contained both ZmGSTF1- and ZmGSTF2-like sequences but was most similar to ZmGSTF1 in detoxifying activity. The expression of TaGSTFs in wheat seedlings was enhanced upon exposure to fenchlorazole ethyl, herbicides or other chemical inducing treatments. TaGSTFs were also enhanced by treatment with the natural products caffeic acid, 7,4-dihydroxyflavone and naringenin. The CDNB-conjugating activity of TaGSTF1, and to a lesser extent TaGSTF6, was highly sensitive to inhibition by flavonoids, particularly the chalcone isoliquiritigenin. The other TaGSTFs were much less sensitive to such inhibition. It was subsequently determined that isoliquiritigenin underwent glutathione conjugation, though this reversible reaction did not require the intervention of any TaGSTF. The potential importance of GSTFs and glutathione conjugation in flavonoid metabolism is discussed.     

FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data

Herein we describe the program FAST-Modelfree for the fully automated, high throughput analysis of NMR spin-relaxation data. This program interfaces with the program Modelfree 4.1 and provides an intuitive graphical user interface for configuration as well as complete standalone operation during the model selection and rotational diffusion parameter optimization processes. FAST-Modelfree is also capable of iteratively assigning models to each spin and optimizing the parameters that describe the diffusion tensor. Tests with the protein Ribonuclease A indicate that using this iterative approach even poor initial estimates of the diffusion tensor parameters will converge to the optimal value within a few iterations. In addition to improving the quality of the final fit, this represents a substantial timesaving compared to manual data analysis and minimizes the chance of human error. It is anticipated that this program will be particularly useful for the analysis and comparison of data collected under different conditions such as multiple temperatures and the presence and absence of ligands. Further, this program is intended to establish a more uniform protocol for NMR spin-relaxation data analysis, facilitating the comparison of results both between and within research laboratories. Results obtained with FAST-Modelfree are compared with previous literature results for the proteins Ribonuclease H, E. coli glutaredoxin-1 and the Ca²⁺-binding protein S100B. These proteins represent data sets collected at both single and multiple static magnetic fields and which required analysis with both isotropic and axially symmetric rotational diffusion tensors. In all cases results obtained with FAST-Modelfree compared favorably with the original literature results.