Size, activity and catabolic diversity of the soil microbial biomass in a wetland complex invaded by reed canary grass

Reed canary grass (Phalaris arundinacea, L.) invasion of wetlands is an ecological issue that has received attention, but its impact on soil microbial diversity is not well documented. The present study assessed the size (substrate-induced respiration), catabolic diversity (CLPP, community level physiological profiles) and composition (selective inhibition) of the soil microbial community in invaded (>95% P. arundinacea cover) and in non-invaded areas of a wetland occupied by native species grown either as a mixed assemblage (22 species) or as quasi-monotypic stands of Scirpus cyperinus (74% cover). The study also tested the hypothesis that decomposition of lignin- and phenolics-rich plant tissues would be fastest in soils exhibiting high catabolic diversity. Results showed that soil respiration, microbial biomass and diversity were significantly higher (P?<?0.03; 1.5 to 3 fold) in P. arundinacea-invaded soils than in soils supporting native plant species. Fungal to bacterial ratios were also higher in invaded (0.6) than in non-invaded (0.4) plots. Further, canonical discriminant analysis of CLPP data showed distinct communities of soil decomposers associated with each plant community. However, these differences in microbial attributes had no effect on decomposition of plant biomass which was primarily controlled by its chemical composition. While P. arundinacea invasion has substantially reduced plant diversity, this study found no parallel decline in the size and diversity of the soil microbial community in the invaded areas.     

Tea, flavonoids and stroke in man and mouse

Background and purpose

To evaluate the strength of the in vivo evidence of relationships between flavonoids and risk of stroke.

Methods

We reviewed the literature more broadly for flavonoids and stroke and conducted an evidence-based review of original publication experiments on tea or tea components on induced coronary occlusion in animal models and on the observational epidemiology on stroke and either tea or flavonoids in man. Each of the studies was evaluated by two independent reviewers. The evidence in total was compared with the Bradford Hill [1] and Stroke Therapy Academic Industry Roundtable (STAIR)¹ quality-assessment criteria [2].

Results

The search of epidemiologic publications revealed 7 cohort studies on flavonoid intake and stroke and 7 cohort studies and 3 case control studies on tea and stroke. In studies of tea there was a consistent protective effect. However, the epidemiologic research on flavonoids and stroke was much less consistent. Eleven animal experiments were identified that examined tea or tea components and stroke relevant sequelae, eight of which reported on infarct volume. All studies demonstrated reduced infarct volumes in animals exposed either to tea extracts, theanine or tea catechins prior to or shortly after reperfusion.

Conclusions

Hill’s criteria of causality are largely met in the case of tea and stroke. A high level of consistency across preclinical studies, of the effect of tea components as single agents effective in reducing stroke volume after middle cerebral artery occlusion, is noted in all rodent models (rat, mouse, and gerbil). Reductions in infarct volume are seen with both tea extracts consumed orally and tea components introduced intra-peritoneally. Observational epidemiology supports this finding in man for tea - the studies are consistent across countries and type of tea and the relative risks are moderately strong. That is not the case for the body of evidence on flavonoid intakes and stroke.     

Multiple copies of functional, Tet(M)-encoding Tn916-like elements in a clinical Enterococcus faecium isolate

Tn916 and similar elements are very common in clinical enterococcal isolates, and are responsible for transmission of a variety of resistance determinants. It is commonly assumed that clinical strains carrying Tn916 have a single copy, although the actual number of copies in clinical isolates has never been systematically studied. We report a clinical isolate of Enterococcus faecium in which three distinct and excision-proficient copies of Tn916-like elements are present in the genome. All of the elements contain tet(M) genes, at least one of which confers resistance to tetracycline and minocycline. Two elements (Tn6085a, Tn6085b) are indistinguishable, containing an inserted 2758 bp Group II intron at the start of open reading frame Tn916ORF_06. The third (Tn6084) also contains the intron, but also has an ISEfa11 integrated upstream of tet(M). All three copies are able to excise from plasmid vectors when cloned in E. coli, and at least two of the elements can transfer to an E. faecium recipient strain. These data indicate that nearly identical Tn916-like elements encoding Tet(M)-mediated tetracycline/minocycline resistance can coexist in clinical E. faecium isolates.     

Problems in using birth certificate files in the capture-recapture model to estimate the completeness of case ascertainment in a population-based birth defects registry in New York State

BACKGROUND: The limitations and underlying assumptions of the capture-recapture methods have hindered their application in epidemiological settings, especially in evaluating the completeness of birth defects registries. This study explored the possibility of using birth certificates as the secondary data source in a simple two-source capture-recapture model to estimate the completeness of case ascertainment of the Congenital Malformations Registry (CMR) for selected major birth defects. METHODS: The CMR and the birth certificates were used as the primary and secondary sources, respectively. Children who were born in 1996-2001 and had selected major birth defects were identified from the two sources. The accuracy of the diagnoses was examined by comparing the individual birth defect categories of the children from the two sources. RESULTS: Discrepancies in birth defect categories in the two data sources and false positives in the birth certificates were the major problems encountered in estimating the completeness of the CMR using the simple two-source capture-recapture method. The estimated completeness for selected major birth defects was only about 71%. Stratified analyses resulted in relatively high estimated completeness for oral clefts (90%) and Down syndrome (88%). CONCLUSIONS Although the birth certificate data was not a good source for estimating the completeness of case ascertainment of the CMR using capture-recapture methods, the analyses provided reasonable estimates for some conditions that were relatively easy to identify and diagnose at birth, such as oral clefts and Down syndrome.     

The cysteine-rich region of T1R3 determines responses to intensely sweet proteins

A wide variety of chemically diverse compounds taste sweet, including natural sugars such as glucose, fructose, sucrose, and sugar alcohols, small molecule artificial sweeteners such as saccharin and acesulfame K, and proteins such as monellin and thaumatin. Brazzein, like monellin and thaumatin, is a naturally occurring plant protein that humans, apes, and Old World monkeys perceive as tasting sweet but that is not perceived as sweet by other species including New World monkeys, mouse, and rat. It has been shown that heterologous expression of T1R2 plus T1R3 together yields a receptor responsive to many of the above-mentioned sweet tasting ligands. We have determined that the molecular basis for species-specific sensitivity to brazzein sweetness depends on a site within the cysteine-rich region of human T1R3. Other mutations in this region of T1R3 affected receptor activity toward monellin, and in some cases, overall efficacy to multiple sweet compounds, implicating this region as a previously unrecognized important determinant of sweet receptor function.     

Real time quantitative PCR as a method to evaluate xenotropic murine leukemia virus removal during pharmaceutical protein purification

Chinese hamster ovary cells used for pharmaceutical protein production express noninfectious retrovirus-like particles. To assure the safety of pharmaceutical proteins, validation of the ability of manufacturing processes to clear retrovirus-like particles is required for product registration. Xenotropic murine leukemia virus (X-MuLV) is often used as a model virus for clearance studies. Traditionally, cell-based infectivity assay has been the standard virus quantification method. In this article, a real time quantitative PCR (Q-PCR) method has been developed for X-MuLV detection/quantification. This method provides accurate and reproducible quantification of X-MuLV particle RNA (pRNA) over a linear dynamic range of at least 100,000-fold with a quantification limit of approximately 1.5 pRNA copies microL(-1). It is about 100-fold more sensitive than the cell-based infectivity assay. High concentrations of protein and cellular DNA present in test samples have been demonstrated to have no impact on X-MuLV quantification. The X-MuLV clearance during chromatography and filtration procedures determined by this method is highly comparable with that determined by the cell-based infectivity assay. X-MuLV clearance measured by both methods showed that anion exchange chromatography (QSFF) and DV50 viral filtration are robust retroviral removal steps. In addition, combination of the two methods was able to distinguish the viral removal from inactivation by the Protein A chromatography, and fully recognize the viral clearance capacity of this step. This new method offers significant advantages over cell-based infectivity assays. It could be used to substitute cell-based infectivity assays for process validation of viral removal procedures, but not inactivation steps. Its availability should greatly facilitate and reduce the cost of viral clearance evaluations for new biologic product development.     

Lycopene and the lung

The human lung, due to the oxidative and ozone stress to which it is exposed, is particularly vulnerable to oxidative damage. Concentrations of dietary antioxidants in the lung epithelial lining and lining fluids may provide protection against oxidative damage. A randomized clinical trial was conducted to study the effects of supplemental, carotenoid-rich vegetable juice (V-8) on lung function macrophage levels of carotenoids and in moderating ozone-induced lung damage. Healthy young adults (n = 23) were exposed to 0.4 ppm ozone in a chamber for 2 hr after either 2 weeks of antioxidant supplementation (including one can of V-8 juice daily) or placebo. Mean lung concentrations of lycopene increased by 12%, and lung epithelial cell DNA damage as measured by the Comet Assay decreased 20% in supplemented subjects. No change in peripheral blood lymphocyte DNA damage was observed as evidenced by no change in mean comet area or length in supplemented or placebo subjects. We were not able to separate the effects of lycopene from other carotenoids or antioxidants administered in this study; however, lycopene is the predominant carotenoid in V-8 (it represents 88% of total carotenoids). A review of the epidemiologic literature providing evidence for the effect of lycopene (diet or serum) or tomatoes on the risk of lung cancer reveals 27 observational epidemiologic studies (18 case-control and nine cohort studies) reporting relative risk (RR) estimates. RR estimates for cohort studies ranged from 0.63 to 1.24 (mean RR = 0.93, SD = 0.16). Odds ratios (OR) for case-control studies ranged from 0.27 to 0.93 (mean OR = 0.61, SD = 0.16). Both plasma levels (RR = 1.01, OR = 0.37) and estimated intakes of lycopene from dietary sources (mean RR = 0.93, RR range = 0.80-1.05; mean OR = 0.67, OR range = 0.27-0.93) were examined. Seventeen studies, three of which were cohorts, reported their results at the level of tomato consumption rather than, or in addition to, lycopene consumption (mean RR = 0.89, RR range = 0.63-1.24; mean OR = 0.61, OR range = 0.37-0.80). The published epidemiologic literature shows an interaction between study design and the relationship between lycopene and/ or tomatoes and risk of lung cancer. Overall, cohort studies did not show an association, whereas case-control studies showed a decreased risk with greater consumption of lycopene and tomatoes. Although lycopene can be found in the human lung, and there is evidence, albeit weak, for a protective association with lung cancer, its biologic role remains to be elucidated.     

A Novel Human Cytomegalovirus Glycoprotein, gpUS9, Which Promotes Cell-to-Cell Spread in Polarized Epithelial Cells, Colocalizes with the Cytoskeletal Proteins E-Cadherin and F-Actin

Processes by which human herpesviruses penetrate and are released from polarized epithelial cells, which have distinct apical and basolateral membrane domains differing in protein and lipid content, are poorly understood. We recently reported that human cytomegalovirus (CMV) mutants with deletions of the gene US9 formed wild-type plaques in cultures of human fibroblasts but were impaired in the capacity for cell-to-cell spread in polarized human retinal pigment epithelial cells. Unlike the glycoproteins that are required for infection, the protein encoded by CMV US9 plays an accessory role by promoting dissemination of virus across cell-cell junctions of polarized epithelial cells. To identify the product and investigate its specialized functions, we selected Madine-Darby canine kidney II (MDCK) epithelial cells that constitutively express CMV US9 or, as a control, US8. The gene products, designated gpUS9 and gpUS8, were glycosylated proteins of comparable molecular masses but differed considerably in intracellular distribution and solubility. Immunofluorescence laser scanning confocal microscopy indicated that, like gpUS8, gpUS9 was present in the endoplasmic reticulum and Golgi compartments of nonpolarized cells. In polarized epithelial cells, gpUS9 also accumulated along lateral membranes, colocalizing with cadherin and actin, and was insoluble in Triton X-100, a property shared with proteins that associate with the cytoskeleton. We hypothesize that gpUS9 may enhance the dissemination of CMV in infected epithelial tissues by associating with the cytoskeletal matrix.     

The Mammalian γ-Tubulin Complex Contains Homologues of the Yeast Spindle Pole Body Components Spc97p and Spc98p

γ-Tubulin is a universal component of microtubule organizing centers where it is believed to play an important role in the nucleation of microtubule polymerization. γ-Tubulin also exists as part of a cytoplasmic complex whose size and complexity varies in different organisms. To investigate the composition of the cytoplasmic γ-tubulin complex in mammalian cells, cell lines stably expressing epitope-tagged versions of human γ-tubulin were made. The epitope-tagged γ-tubulins expressed in these cells localize to the centrosome and are incorporated into the cytoplasmic γ-tubulin complex. Immunoprecipitation of this complex identifies at least seven proteins, with calculated molecular weights of 48, 71, 76, 100, 101, 128, and 211 kD. We have identified the 100- and 101-kD components of the γ-tubulin complex as homologues of the yeast spindle pole body proteins Spc97p and Spc98p, and named the corresponding human proteins hGCP2 and hGCP3. Sequence analysis revealed that these proteins are not only related to their respective homologues, but are also related to each other. GCP2 and GCP3 colocalize with γ-tubulin at the centrosome, cosediment with γ-tubulin in sucrose gradients, and coimmunoprecipitate with γ-tubulin, indicating that they are part of the γ-tubulin complex. The conservation of a complex involving γ-tubulin, GCP2, and GCP3 from yeast to mammals suggests that structurally diverse microtubule organizing centers such as the yeast spindle pole body and the animal centrosome share a common molecular mechanism for microtubule nucleation.