Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline.

Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH4+, further supporting the idea of AOA favouring lower soil NH4+ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.

Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors.

Ammonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author's knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW.

Commensal enteric bacteria lipopolysaccharide impairs host defense against disseminated Candida albicans fungal infection.

Commensal enteric bacteria maintain systemic immune responsiveness that protects against disseminated or localized infection in extra-intestinal tissues caused by pathogenic microbes. However, as shifts in infection susceptibility after commensal bacteria eradication have primarily been probed using viruses, the broader applicability to other pathogen types remains undefined. In sharp contrast to diminished antiviral immunity, we show commensal bacteria eradication bolsters protection against disseminated Candida albicans fungal infection. Enhanced antifungal immunity reflects more robust systemic expansion of Ly6G(hi)Ly6C(int) neutrophils, and their mobilization into infected tissues among antibiotic-treated compared with commensal bacteria-replete control mice. Reciprocally, depletion of neutrophils from expanded levels or intestinal lipopolysaccharide reconstitution overrides the antifungal protective benefits conferred by commensal bacteria eradication. This discordance in antifungal compared with antiviral immunity highlights intrinsic differences in how commensal bacteria control responsiveness for specific immune cell subsets, because pathogen-specific CD8(+) T cells that protect against viruses were suppressed similarly after C. albicans and influenza A virus infection. Thus, positive calibration of antiviral immunity by commensal bacteria is counterbalanced by restrained activation of other immune components that confer antifungal immunity.

In vitro anti-caries effect of fluoridated hydroxyapatite-coated preformed metal crowns.

AIM: To synthesise fluoridated hydroxyapatite (FA) crystals directly on preformed metal crowns (PMCs) and evaluate the anti-cariogenic properties in an in vitro model. METHODS: FA crystals were grown on etched PMCs and stainless steel discs and characterised by SEM. FA-coated discs allowed fluoride release to be assessed from a known surface area of FA crystals. Discs were divided into four groups (n = 6/group) and exposed to solutions at pH 4-7. Fluoride levels in solution were measured after each exposure. Twelve FA-coated and 12 non-coated PMCs were cemented onto human molars using glass ionomer (GI) or unfilled resin, making four groups of six teeth; FA-coated + GI, FA-coated + resin; non-coated + GI and non-coated + resin. Teeth were exposed to acidified gelatin (pH = 4.3) for 9 weeks. RESULTS: SEM showed FA crystal growth on interior and exterior of the crowns. Average fluoride release from FA-coated discs was 0.16 mg/L/cm² at pH < 5.0. Teeth were sectioned through the lesion. Polarised microscopic examination revealed significantly smaller lesions in FA-coated crown groups compared to non-coated crown groups. CONCLUSION: FA-coated PMCs demonstrated carious lesion preventing effects, i.e. fluoride release and reduction of demineralisation at crown/tooth interface. FA-coated crowns could be an aesthetic, inexpensive and caries preventive alternative in clinical dentistry.

DDT and the decline of free-tailed bats (Tadarida brasiliensis) at Carlsbad Cavern, New Mexico.

DDT is believed to have caused the population of Brazilian free-tailed bats (Tadarida brasiliensis mexicana) at Carlsbad Cavern to decline severely after 1936. Nevertheless, previous data supporting this hypothesis are limited to a single study from 1974, which indicated that 20% of young free-tails from the cavern may have died of DDE poisoning during their first southward migration. In this study I compared organochlorine residues among samples of free-tails collected in Carlsbad Cavern in 1930, 1956, 1965, 1973, and 1988. Samples of skin cut from dry museum specimens were chemically analyzed, except for the 1973 data, which were derived from analyses of whole bats minus gastrointestinal tracts. Accumulated residue levels of DDT compounds in bats from 1965 and 1956 exceeded those in 1973 bats by approximately 4.8 times and approximately 2.7 times, respectively. This suggests that lethal effects of DDT compounds were substantially greater in the 1950s and 1960s than in the 1970s. Residues in 1988 bats resembled those for 1973 bats. It is concluded that DDT played a major role in this severe population decline. These results can be applied by management personnel in evaluating the present and future status of this population regarding persisting organochlorine insecticides as well as other agricultural chemicals now in use. The case of the Carlsbad colony is discussed relative to the general issue of other bat population declines.

Impaired progenitor cell function in HIV-negative infants of HIV-positive mothers results in decreased thymic output and low CD4 counts.

Hematologic and immunologic functions were examined in 19 HIV-negative infants of HIV-positive mothers and 19 control infants of HIV-negative mothers. Control infants were selected to match for gestational age, weight, and mode of delivery. Cord blood was obtained from all infants and used for flow cytometric determination of lymphocyte subsets, including the naive CD4 count. Furthermore, to determine thymic output, cord blood mononuclear cells were used for determination of T-cell receptor excision circles (TRECs). Evaluation of progenitor cell function was done by means of colony-forming cell assay and fetal thymic organ cultures (FTOCs). Lower naive CD4 counts (459.3 +/- 68.9 vs 1128.9 +/- 146.8 cells/microL, P <.001) and reduced thymic output in infants of HIV-positive mothers were found (frequency of CD4(+) cells with TRECs was 3.6% +/- 0.7% compared with 14.3% +/- 2.2% in controls, P <.001). In combination with lower red blood cell counts in infants of HIV-positive mothers, this finding suggested impairment of progenitor cell function. Indeed, progenitors from infants of HIV-positive mothers had decreased cloning efficiency (15.7% +/- 2.6% vs 55.8% +/- 15.9%, P =.009) and seemed to generate fewer T cells in FTOCs. In conclusion, lower numbers of naive CD4(+) cells and reduced thymic output in HIV-negative infants of HIV-positive mothers may be due to impaired progenitor cell function.

Grignard reactions of 4-substituted-2-keto-1,3-dioxanes: highly diastereoselective additions controlled by a remote alkyl group.

[see reaction]. The reactions of Grignard reagents with a representative series of simple cis-2-keto-4-substituted-1,3-dioxanes have been investigated. The stereochemical outcome of these highly diastereoselective additions (dr > 90:10) is consonant with Cram's chelate model on the assumption that RMgX coordinates preferentially with the ring oxygen remote from the C(4) substituent.

Dicofol residues in eggs and carcasses of captive American kestrels.

American kestrels (Falco sparverius) were fed diets containing 0 (control), 1, 3, 10, and 30 microgram/g (wet wt) of Kelthane. Residues of dicofol and its metabolites were then analyzed in the eggs and carcasses of females. Significant differences occurred among treatments for residues of both p,p'-dicofol and p,p'-dechlorodicofol (DCD) in both eggs and carcasses and for p,p'-dicholorbenzophenone (DCBP) in eggs. Residue concentrations increased with increasing treatment exposure. Residues of p,p'-dicofol, p,p'-DCD, and p,p'-DCBP in eggs were significantly correlated with eggshell quality parameters. Significant correlations also occurred among contaminants in eggs and for individual contaminants between eggs and carcasses. The lowest-observed-dietary-effect concentration for eggshell thinning was 3 microgram/g, whereas 1 microgram/g may be considered to be near a no-observable-adverse-effect concentration. Concentrations of dicofol in potential prey items and eggs of wild birds generally have been lower than dietary-effect concentrations or concentrations in tissues or eggs associated with eggshell thinning and reduced reproductive success.

T-cell progenitor function during progressive human immunodeficiency virus-1 infection and after antiretroviral therapy.

Impairment of T-cell renewal has been proposed as contributing to CD4(+) T-cell depletion in persons infected with human immunodeficiency virus-1. We analyzed the T-cell development capacity of progenitors using fetal thymus organ culture. Those who progressed to AIDS had a dramatic loss in T-cell development capacity shortly after seroconversion. In contrast, long-term nonprogressors retained progenitor capacity 8 years after seroconversion. Approximately 70% of patients experienced an improvement in T-cell development capacity after receiving 6 months of potent antiretroviral therapy. Improvement in T-cell development in fetal thymus organ culture correlated with an increase in the number of naive CD4(+) T cells in peripheral blood. Numbers of progenitors in blood and bone marrow after seroconversion or during therapy did not correlate with the change observed in T-cell development capacity. These data provide evidence that HIV-1 infection can interfere with T-cell renewal at the level of the progenitor cell. Interference with T-cell renewal may contribute to CD4(+) T-cell depletion.

The relationship between the dissolved inorganic carbon concentration and growth rate in marine phytoplankton.

A range of marine phytoplankton was grown in closed systems in order to investigate the kinetics of dissolved inorganic carbon (DIC) use and the influence of the nitrogen source under conditions of constant pH. The kinetics of DIC use could be described by a rectangular hyperbolic curve, yielding estimations of KG(DIC) (the half saturation constant for carbon-specific growth, i.e. C mu) and mu max (the theoretical maximum C mu). All species attained a KG(DIC) within the range of 30-750 microM DIC. For most species, NH4+ use enabled growth with a lower KG(DIC) and/or, for two species, an increase in mu max. At DIC concentrations of > 1.6 mM, C mu was > 90% saturated for all species relative to the rate at the natural seawater DIC concentration of 2.0 mM. The results suggest that neither the rate nor the extent of primary productivity will be significantly limited by the DIC in the quasi-steady-state conditions associated with oligotrophic oceans. The method needs to be applied in the conditions associated with dynamic coastal (eutrophic) systems for clarification of a potential DIC rate limitation where cells may grow to higher densities and under variable pH and nitrogen supply.

Treatment with granulocyte colony-stimulating factor decreases the capacity of hematopoietic progenitor cells for generation of lymphocytes in human immunodeficiency virus-infected persons.

An obstacle to stem cell gene therapy for AIDS is the limited numbers of hematopoietic progenitors available. Granulocyte colony-stimulating factor (G-CSF) is used for mobilization of progenitors, but little is known about the functional characteristics of mobilized progenitors, and immature and T cell progenitors may not be mobilized. This study examined the effect of G-CSF on the function of progenitors. Ten human immunodeficiency virus-infected patients received G-CSF (filgrastim, 300 microgram/day) for 5 days. Absolute numbers of immature and T cell progenitors did not increase. The ability of CD34+ progenitor cells to generate lymphocytes was examined by use of thymic organ cultures. The mean number of lymphocytes generated per CD34+ cell on day 0 was 0.72 and on day 4 was 0.09 (P<.003). The number of CD4+ cells generated per CD34+ cell was significantly reduced after G-CSF treatment. Thus, G-CSF increased the number of mature progenitor cells but did not increase T cell progenitors.

Utilization of dissolved inorganic carbon (DIC) and the response of the marine flagellate Isochrysis galbana to carbon or nitrogen stress.

The growth of the marine flagellate Isochrysis galbana was followed in batch cultures at four concentrations of dissolved inorganic carbon (DIC), from C- and N-replete lag phase into C- and/or N-deplete stationary phase. Organic buffers were omitted from the growth medium, and culture pH was maintained at 8.30±0.05 by the addition of acid or alkali. The responses of the flagellate to N stress included an increase in the C∶N ratio, and decreases in the ratios of glutamine (Gln)∶glutamate (Glu) and Chl a∶C, and the cell Chl a quota. Conversely, the responses to C stress included a decrease in the C∶N ratio, and increases in the ratios of Gln∶Glu and Chl a∶C, and the cell Chl a quota. The relationship between carbon-specific growth rate (C-µ), and the concentration of extracellular DIC, [DIC]ext , exhibited Michaelis-Menten type kinetics with a half saturation constant, KG(DIC) , of 81 µM. Comparative studies of the diatom Phaeodactylum tricornutum showed similar results, although the value of KG(DIC) was lower at 30 µM.

Restriction endonucleases in clinical isolates of Shigella spp.

Thirteen restriction endonuclease-containing strains were isolated from a collection of 186 clinical isolates of Shigella spp. Among these, eight and five isolates carried isoschizomers of EcoRII and NciI, respectively. The former restriction-modification (R-M) system was homologous to that of EcoRII and was located on plasmids with sizes of 46.6 or 55.6 kb. Isolates producing NciI isoschizomers contained a 5.7-kb non-transferable plasmid. Together with antimicrobial susceptibility tests and plasmid profile studies, it is concluded that these two R-M systems are not widely spread but confined to strains with similar antibiotic resistance and plasmid profile.

Peripheral blood from human immunodeficiency virus type 1-infected patients displays diminished T cell generation capacity.

An organ culture chimera system was used to assess the effect of human immunodeficiency virus type 1 (HIV-1) infection on the T cell-generation capacity of precursors derived from human peripheral blood. Peripheral blood mononuclear cells from HIV-1-infected patients and uninfected controls were placed on fetal thymus lobes of NOD/LtSz-scid/scid mice. Blood from the HIV-1-infected patients consistently produced fewer CD4 and CD8 cells compared with blood from controls (P < .01). Addition of zidovudine to the cultures did not alter this profile. Limit dilution experiments suggested that there were fewer functional precursors in the infected patients. These results were not dependent on the patient's level of peripheral CD4 cells; even samples from patients with normal CD4 cell counts were unable to generate T cells in organ cultures. The results are consistent with a loss in the capacity of HIV-1-infected patients to produce functional T cell progenitors in their peripheral blood.

Noninvasive positive pressure ventilation.

Noninvasive positive pressure ventilation (NPPV) has been used in treatment of a variety of clinical conditions, including acute respiratory failure (ARF) due to status asthmaticus. We present the case of a patient admitted with acute exacerbation of asthma who had ARF and required mechanical ventilation. After extubation, he had respiratory distress and was successfully treated with NPPV. NPPV was continued for approximately 24 hours, with clinical improvement and avoidance of reintubation. Despite the benefits of NPPV (ie, improved patient comfort, reduced need for sedation, and avoidance of complications associated with mechanical ventilation), it has not been widely used. Understanding the clinical indications for and limitations of NPPV allows successful use of this noninvasive method of mechanical ventilation.

Development of CD4 and CD8 single positive T cells in human thymus organ culture: IL-7 promotes human T cell production by supporting immature T cells.

This paper describes novel model systems to study the development of human T cells. Fragments of neonatal human thymus (HUNT) can be cultured in vitro; the initial majority population of CD4, CD8 double-positive (DP) thymocytes is not maintained in organ culture. These cells are rapidly replaced by populations of CD4 or CD8 single-positive (SP) T cells. In addition, allogeneic thymic chimeras can be established by the addition of human cord blood (HUCB) mononuclear cells as a source of T progenitor cells to the organ cultures. Culture results in the acquisition of a mature SP T cell phenotype by the donor cells similar to that found when HUCB is allowed to develop in xenogeneic murine scid/scid fetal thymus organ culture. The number of immature and mature T cells produced by organ cultures can be differentially increased by the addition of exogenous IL-7, stem cell growth factor, IL-1, or GM-CSF. Anti-IL-7 antibody inhibits T cell production. Taken together, the results suggest that human T cell development occurs in these in vitro systems in a similar manner, regardless of the species origin of the thymic stromal cells in the culture, and that exogenous cytokines can be used to expand subpopulations of developing T cells.

Organochlorine residues in bat guano from nine Mexican caves, 1991.

: Samples of bat guano, primarily from Mexican free-tailed bats (Tadarida brasiliensis), were collected at nine bat roosts in caves in northern and eastern Mexico and analysed for organochlorine residues. DDE, the most abundant residue found in each cave, was highest (0.99 p.p.m. dry weight) at Ojuela Cave, Durango. Other studies of DDE in bat guano indicate that this concentration is too low to reflect harmful concentrations in the bats themselves. The DDE at Ojuela may represent either lingering residues from use of DDT years ago in the Ojuela area of perhaps depuration loss from migrant bats with summer maternity roost(s) in a DDE-contaminated area such as Carlsbad Cavern, New Mexico. Presence of o,p'-DDT at Tio Bartolo Cave, Nuevo Leon, indicates recent use of DDT, but the concentration of this contaminant was low. Possible impacts on bat colonies of the organophosphorus and carbamate insecticides now in extensive use are unknown.