Detecting Allosteric Networks Using Molecular Dynamics Simulation

Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules.

Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae

A novel obligate methylamine utilizer (strain JLW8(T)), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5-8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C(16 : 0)omega7c and C(16 : 0) and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97-98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93-96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8(T) (=ATCC BAA-1282(T)=DSM 17540(T)) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.

Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates

The taxonomic positions and phylogenetic relationships of two new methylotrophic isolates from Lake Washington (USA) sediment, FAM5Tand 500, and the previously described methylotrophic strain EHg5 isolated from contaminated soil in Estarreja (Portugal) were investigated. All three strains were facultative methylotrophs capable of growth on a variety of C1and multicarbon compounds. Optimal growth occurred at pH 7.5–8 and 30–37 °C. The major fatty acids were C16 : 1ω7cand C16 : 0. The major quinone was ubiquinone Q8. Neither methanol dehydrogenase nor methanol oxidase activities were detectable in cells grown on methanol, suggesting an alternative, as-yet unknown, mechanism for methanol oxidation. The isolates assimilated C1units at the level of formaldehyde, via the serine cycle. The DNA G+C content of the strains ranged between 64 and 65 mol%. 16S rRNA gene sequence similarity between the three new isolates was 99.85–100 %, but was below 94 % with other members of theBetaproteobacteria, indicating that the isolates represent a novel taxon. Based on physiological, phenotypic and genomic characteristics of the three isolates, a new genus,Methyloversatilisgen. nov., is proposed within the familyRhodocyclaceae. The type strain ofMethyloversatilis universalisgen. nov., sp. nov. is FAM5T(=CCUG 52030T=JCM 13912T).

Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations

A fluorescence in situ hybridization-flow cytometry (FISH/FC)-based method was optimized using artificial mixtures of pure cultures of methanotrophic bacteria. Traditional oligonucleotide probes targeting 16S rRNAs of type I (MG84/705 probe) and type II (MA450 probe) methanotrophs were labeled with fluorescein or Alexa fluor and used for FISH, followed by fluorescence-activated FC analysis and cell sorting (FACS). The method resulted in efficient separation of target cells (type I or type II methanotrophs) from the artificial mixtures. The method was then applied for detection and enrichment of type I and type II methanotroph populations from a natural sample, Lake Washington sediment. Cells were extracted from the sediment, fixed, and subjected to FISH/FC/FACS. The resulting subpopulations were analyzed by reverse transcriptase PCR surveys of 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde-activating enzyme) genes. The functional gene analysis indicated specific separation of the type I and type II methanotroph populations. 16S rRNA gene analysis revealed that type I methanotrophs comprised 59% of the subpopulation separated using the type I-specific probe and that type II methanotrophs comprised 47.5% of the subpopulation separated using the type II-specific probe. Our data indicate that the FISH/FC/FACS protocol described can provide significant enrichment of microbial populations of interest from complex natural communities and that these can be used for genetic tests. We further tested the possibility of direct whole-genome amplification (WGA) from limited numbers of sorted cells, using artificial mixtures of microbes whose genome sequences are known. We demonstrated that efficient WGA can be achieved using 10(4) or more cells separated by 16S rRNA-specific FISH/FC/FACS, while fewer cells resulted in less specific WGA.

Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detection

The origins and the evolutionary history of tetrahydromethanopterin-linked C1 transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. In previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated Proteobacteria, Planctomycetes, or Archaea (M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova, Microb. Ecol. 48:463-472, 2004; M. G. Kalyuzhnaya, O. Nercessian, M. E. Lidstrom, and L. Chistoserdova, Environ. Microbiol. 7:1269-1274, 2005). Here we used a metagenomic approach to demonstrate that these divergent genes are present with high abundance in the microbial community inhabiting Lake Washington sediment. We also gained preliminary insights into the genomic composition of the organisms possessing these genes by sequencing genomic fragments from three uncultured microbes possessing the genes of interest. Phylogenetic analyses suggested that, although distantly related to each other, these organisms deeply diverge from known Bacteria and Archaea, with more relation to the former, suggesting their affiliation with a new bacterial phylum. We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling.

Implementation of a primary care physician network obesity management program

Most primary care physicians do not treat obesity, citing lack of time, resources, insurance reimbursement, and knowledge of effective interventions as significant barriers. To address this need, a 10-minute intervention delivered by the primary care physician was coupled with individual dietary counseling sessions delivered by a registered dietitian via telephone with an automated calling system (House-Calls, Mobile, AL). Patients were seen for follow-up by their physician at weeks 4, 12, 24, 36 and 52. A total of 252 patients (202 women and 50 men) were referred by 18 primary care physicians to the program. The comorbid conditions reported for all patients at baseline included low back pain, 29% (n = 72); hypertension, 45% (n = 113); hypercholesterolemia, 41% (n = 104); type 2 diabetes, 10% (n = 26); and sleep apnea, 5% (n = 12). When offered a choice of meal plans based on foods or meal replacements, two-thirds of patients (n = 166) chose to use meal replacements (Ultra Slim-Fast; Slim-Fast Foods Co., West Palm Beach, FL) at least once daily. Baseline weights of subjects averaged 200 +/- 46 lb for women (n = 202) and 237 +/- 45 lb for men (n = 50). Patients completing 6 months in the program lost an average of 19.0 +/- 4.0 lb for women (n = 94) and 15.5 +/- 8.2 lb for men (n = 26). Physicians reported a high degree of satisfaction with the program, suggesting that a brief, effective physician-directed program with nutritionist support by telephone can be implemented in a busy primary care office.

Applying science to changing dietary patterns

The intake of 400-600 g/d of fruits and vegetables is associated with reduced incidence of many common forms of cancer. These foods contain phytochemicals that can modulate gene expression to inhibit carcinogenesis via multiple pathways. Many phytochemicals are colorful, providing an easy way to communicate increased diversity of fruits and vegetables to the public. Red foods contain lycopene, the pigment in tomatoes, which is localized in the prostate gland and may be involved in maintaining prostate health. Yellow-green vegetables, such as corn and leafy greens, contain lutein and zeaxanthin, which are localized in the retina where age-related macular degeneration occurs. Red-purple foods contain anthocyanins, which are powerful antioxidants found in red apples, grapes, berries and wine. Orange foods, including carrots, mangos, apricots, pumpkin and winter squash, contain beta-carotene. Orange-yellow foods, including oranges, tangerines and lemons contain citrus flavonoids. Green foods, including broccoli, Brussels sprouts and kale, contain glucosinolates. White-green foods in the onion family contain allyl sulfides. Consumers are advised to ingest one serving of each of the above groups daily, putting this recommendation within the National Cancer Institute and American Institute for Cancer Research guidelines of five to nine servings per day. The color code provides simplification, but it is also important as a way to help consumers to find common fruits and vegetables easily while traveling, eating in restaurants or working. At home, simple ways of preparing foods rapidly and easily are needed to influence dietary patterns.

An analysis of nine proprietary Chinese red yeast rice dietary supplements: implications of variability in chemical profile and contents

OBJECTIVES

Some strains of Chinese red yeast rice, when prepared by solid fermentation, produce compounds called monacolins that inhibit cholesterol production. When used as a dietary supplement to achieve and maintain healthy cholesterol levels, Chinese red yeast rice has significant potential to reduce health care costs and contribute to public health by reducing heart disease risk in individuals with moderate elevations of circulating cholesterol levels. Whereas one proprietary strain of Chinese red yeast rice has been demonstrated to lower cholesterol levels significantly in clinical trials, other strains being sold as Chinese red yeast rice dietary supplements have not undergone similar evaluation. In order to determine whether the results of a clinical trial conducted with one strain of Chinese red yeast rice could be generalized to other preparations of Chinese red yeast rice, nine different commercially available dietary supplements were purchased tested for chemical constituents.

DESIGN

Monacolins were measured by high performance liquid chromatography (HPLC) that separates the various monacolins in Chinese red yeast rice. Citrinin concentration, a toxic fermentation byproduct, was measured by radioimmunoassay.

RESULTS

Total monacolin content varied from 0% to 0.58% w/w and only 1 of 9 preparations had the full complement of 10 monacolin compounds. Citrinin was found at measurable concentrations in 7 of the 9 preparations.

CONCLUSIONS

The findings from clinical trials demonstrating significant and clinically relevant cholesterol reduction using a defined Chinese red yeast rice preparation containing 10 different monacolins cannot be generalized to preparations that do not contain the same levels and profile of monacolins. Standardized manufacturing practices should be established for Chinese red yeast rice sold as a dietary supplement in order ensure equivalence of content of active ingredients in preparations being sold to the public and to limit the production of unwanted byproducts of fermentation such as citrinin. In common with other botanical dietary supplements, the full potential of this product will not be realized until standards for production and labeling of Chinese red yeast rice are further developed.