The application of the herbicide bromoxynil to a model soil-derived bacterial community: impact on degradation and community structure

AIMS: Bromoxynil degradation by soil micro-organisms has been shown to be co-oxidative in character. In this study, we investigate both the impact of the application of increasing bromoxynil concentrations on soil-derived bacterial communities and how these changes are reflected in the degradation of the compound. Our aim was to test the hypothesis that the addition of bromoxynil to a soil-derived bacterial community, and the availability of a readily utilizable carbon source would have an impact on bromoxynil degradation, and that would be reflected in the bacteria present in the soil community. METHODS AND RESULTS: Degradation of bromoxynil was observed in soil-derived communities containing 15 mg l(-1), but not 50 mg l(-1) of the compound, unless glucose was added. This suggests that the addition of carbon stimulates co-oxidative bromoxynil degradation by the members of the bacterial community. Measurable changes in the bacterial community indicated that the addition of bromoxynil led to deterministic selection on the bacterial population, i.e. the communities observed arise through the selection of specific micro-organisms that are best adapted to the conditions in the soil. The addition of bromoxynil was also shown to have a negative impact on the presence of alpha and gamma-proteobacteria in the soil community. CONCLUSION: Bromoxynil degradation is significantly inhibited in bacterial soil communities in the absence of readily accessible carbon. The application of bromoxynil appears to exert deterministic selection on the bacterial community. SIGNIFICANCE AND IMPACT OF THE STUDY: This study highlights the effects of increasing bromoxynil concentrations on a model bacterial population derived from soil. Soil communities show qualitative and quantitative differences to bromoxynil application depending on the availability of organic carbon. These findings might have implications for the persistence of bromoxynil in agricultural soils.     

EspF of enteropathogenic Escherichia coli binds sorting nexin 9

EspF of enteropathogenic Escherichia coli targets mitochondria and subverts a number of cellular functions. EspF consists of six putative Src homology 3 (SH3) domain binding motifs. In this study we identified sorting nexin 9 (SNX9) as a host cell EspF binding partner protein, which binds EspF via its amino-terminal SH3 region. Coimmunoprecipitation and confocal microscopy showed specific EspF-SNX9 interaction and non-mitochondrial protein colocalization in infected epithelial cells.     

The impact of acrylonitrile and bioaugmentation on the biodegradation activity and bacterial community structure of a topsoil

The analysis of the bacterial community within the soil using DGGE showed acrylonitrile (ACN) could lead to the selection of significantly similar communities. Moreover, Rhodococcus sp. AJ270 was successfully established in the soil community. High GC G+-bacteria also responded positively to ACN addition. Bioaugmentation or carbon addition had no impact on the rate or degree of ACN degradation. ACN could be readily degraded by the soil bacteria, however, the community structure was significantly affected by its addition as well as by the addition of carbon or Rhodococcus sp. AJ270. The bioaugmentation of the soil with this strain was successful, in that the organism became established within the community. ACN addition to a soil produces statistically significant changes in the bacterial community.     

The current and future applications of microorganism in the bioremediation of cyanide contamination

Inorganic cyanide and nitrile compounds are distributed widely in the environment, chiefly as a result of anthropogenic activity but also through cyanide synthesis by a range of organisms including higher plants, fungi and bacteria. The major source of cyanide in soil and water is through the discharge of effluents containing a variety of inorganic cyanide and nitriles. Here the fate of cyanide compounds in soil and water is reviewed, identifying those factors that affect their persistence and which determine whether they are amenable to biological degradation. The exploitation of cyanides by a variety of taxa, as a mechanism to avoid predation or to inhibit competitors has led to the evolution in many organisms of enzymes that catalyse degradation of a range of cyanide compounds. Microorganisms expressing pathways involved in cyanide degradation are briefly reviewed and the current applications of bacteria and fungi in the biodegradation of cyanide contamination in the field are discussed. Finally, recent advances that offer an insight into the potential of microbial systems for the bioremediation of cyanide compounds under a range of environmental conditions are identified, and the future potential of these technologies for the treatment of cyanide pollution is discussed.     

Glucose sensing by gut endocrine cells and activation of the vagal afferent pathway is impaired in a rodent model of type 2 diabetes mellitus

Glucose in the gut lumen activates gut endocrine cells to release 5-HT, glucagon-like peptide 1/2 (GLP-1/2), and glucose-dependent insulinotropic polypeptide (GIP), which act to change gastrointestinal function and regulate postprandial plasma glucose. There is evidence that both release and action of incretin hormones is reduced in type 2 diabetes (T2D). We measured cellular activation of enteroendocrine and enterochromaffin cells, enteric neurons, and vagal afferent neurons in response to intestinal glucose in a model of type 2 diabetes mellitus, the UCD-T2DM rat. Prediabetic (PD), recent-diabetic (RD, 2 wk postonset), and 3-mo diabetic (3MD) fasted UCD-T2DM rats were given an orogastric gavage of vehicle (water, 0.5 ml /100 g body wt) or glucose (330 μmol/100 g body wt); after 6 min tissue was removed and cellular activation was determined by immunohistochemistry for phosphorylated calcium calmodulin-dependent kinase II (pCaMKII). In PD rats, pCaMKII immunoreactivity was increased in duodenal 5-HT (P < 0.001), K (P < 0.01) and L (P < 0.01) cells in response to glucose; glucose-induced activation of all three cell types was significantly reduced in RD and 3MD compared with PD rats. Immunoreactivity for GLP-1, but not GIP, was significantly reduced in RD and 3MD compared with PD rats (P < 0.01). Administration of glucose significantly increased pCaMKII in enteric and vagal afferent neurons in PD rats; glucose-induced pCaMKII immunoreactivity was attenuated in enteric and vagal afferent neurons (P < 0.01, P < 0.001, respectively) in RD and 3MD. These data suggest that glucose sensing in enteroendocrine and enterochromaffin cells and activation of neural pathways is markedly impaired in UCD-T2DM rats.     

Glycoforms of UT-A3 urea transporter with poly-N-acetyllactosamine glycosylation have enhanced transport activity

Urea transporters UT-A1 and UT-A3 are both expressed in the kidney inner medulla. However, the function of UT-A3 remains unclear. Here, we found that UT-A3, which comprises only the NH(2)-terminal half of UT-A1, has a higher urea transport activity than UT-A1 in the oocyte and that this difference was associated with differences in N-glycosylation. Heterologously expressed UT-A3 is fully glycosylated with two glycoforms of 65 and 45 kDa. By contrast, UT-A1 expressed in HEK293 cells and oocytes exhibits only a 97-kDa glycosylation form. We further found that N-glycans of UT-A3 contain a large amount of poly-N-acetyllactosamine. This highly glycosylated UT-A3 is more stable and is enriched in lipid raft domains on the cell membrane. Kifunensine, an inhibitor of α-mannosidase that inhibits N-glycan processing beyond high-mannose-type N-glycans, significantly reduced UT-A3 urea transport activity. We then examined the native UT-A1 and UT-A3 glycosylation states from kidney inner medulla and found the ratio of 65 to 45 kDa in UT-A3 is higher than that of 117 to 97 kDa in UT-A1. The highly stable expression of highly glycosylated UT-A3 on the cell membrane in kidney inner medulla suggests that UT-A3 may have an important function in urea reabsorption.     

Functional Glycomic Analysis of Human Milk Glycans Reveals the Presence of Virus Receptors and Embryonic Stem Cell Biomarkers

Human milk contains a large diversity of free glycans beyond lactose, but their functions are not well understood. To explore their functional recognition, here we describe a shotgun glycan microarray prepared from isolated human milk glycans (HMGs), and our studies on their recognition by viruses, antibodies, and glycan-binding proteins (GBPs), including lectins. The total neutral and sialylated HMGs were derivatized with a bifunctional fluorescent tag, separated by multidimensional HPLC, and archived in a tagged glycan library, which was then used to print a shotgun glycan microarray (SGM). This SGM was first interrogated with well defined GBPs and antibodies. These data demonstrated both the utility of the array and provided preliminary structural information (metadata) about this complex glycome. Anti-TRA-1 antibodies that recognize human pluripotent stem cells specifically recognized several HMGs that were then further structurally defined as novel epitopes for these antibodies. Human influenza viruses and Parvovirus Minute Viruses of Mice also specifically recognized several HMGs. For glycan sequencing, we used a novel approach termed metadata-assisted glycan sequencing (MAGS), in which we combine information from analyses of glycans by mass spectrometry with glycan interactions with defined GBPs and antibodies before and after exoglycosidase treatments on the microarray. Together, these results provide novel insights into diverse recognition functions of HMGs and show the utility of the SGM approach and MAGS as resources for defining novel glycan recognition by GBPs, antibodies, and pathogens.     

Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly

The decline in activity energy expenditure underlies a range of age-associated pathological conditions, neuromuscular and neurological impairments, disability, and mortality. The majority (90%) of the energy needs of the human body are met by mitochondrial oxidative phosphorylation (OXPHOS). OXPHOS is dependent on the coordinated expression and interaction of genes encoded in the nuclear and mitochondrial genomes. We examined the role of mitochondrial genomic variation in free-living activity energy expenditure (AEE) and physical activity levels (PAL) by sequencing the entire (~16.5 kilobases) mtDNA from 138 Health, Aging, and Body Composition Study participants. Among the common mtDNA variants, the hypervariable region 2 m.185G>A variant was significantly associated with AEE (p=0.001) and PAL (p=0.0005) after adjustment for multiple comparisons. Several unique nonsynonymous variants were identified in the extremes of AEE with some occurring at highly conserved sites predicted to affect protein structure and function. Of interest is the p.T194M, CytB substitution in the lower extreme of AEE occurring at a residue in the Qi site of complex III. Among participants with low activity levels, the burden of singleton variants was 30% higher across the entire mtDNA and OXPHOS complex I when compared to those having moderate to high activity levels. A significant pooled variant association across the hypervariable 2 region was observed for AEE and PAL. These results suggest that mtDNA variation is associated with free-living AEE in older persons and may generate new hypotheses by which specific mtDNA complexes, genes, and variants may contribute to the maintenance of activity levels in late life.     

Amphiphiles for supercritical CO2

A semi-fluorinated hybrid amphiphile, pentadecafluoro-5-dodecyl (F7H4) sulfate, has been shown to form reversed micelles in dense CO₂; the aggregates evolve to form water-in-CO₂ (w/c) microemulsion droplets on addition of water. Aggregation structures in these w/c phases have been characterised by small-angle neutron scattering (SANS), showing the presence of cylindrical droplets, which change into dispersed lamellar phases at even higher water loadings. Other systems are also introduced, being high internal phase emulsions (HIPEs) with brine, and liquid and supercritical CO₂, stabilized by certain commercially available nonylphenol ethoxylates (Dow Tergitol NP-, and Huntsman Surfonic N- amphiphiles). These dispersions have been characterised by SANS for the first time. Quantitative analyses of the HIPEs SANS profiles show that they behave similarly to hydrocarbon-water emulsion analogues, with regard to total interfacial areas and the effects of amphiphile concentration on the underlying structures. Finally, the advantages and disadvantages of both approaches for controlling the physico-chemical properties of liquid/supercritical CO₂ in potential applications are compared and contrasted. These results highlight the importance of using specially designed CO₂-philic amphiphiles for generating self-assembly structures in dense CO₂.     

Analysis of Biochemical Equilibria Relevant to the Immune Response: Finding the Dissociation Constants

This paper analyzes the biochemical equilibria between bivalent receptors, homo-bifunctional ligands, monovalent inhibitors, and their complexes. Such reaction schemes arise in the immune response, where immunoglobulins (bivalent receptors) bind to pathogens or allergens. The equilibria may be described by an infinite system of algebraic equations, which accounts for complexes of arbitrary size n (n being the number of receptors present in the complex). The system can be reduced to just 3 algebraic equations for the concentrations of free (unbound) receptor, free ligand and free inhibitor. Concentrations of all other complexes can be written explicitly in terms of these variables. We analyze how concentrations of key (experimentally-measurable) quantities vary with system parameters. Such measured quantities can furnish important information about dissociation constants in the system, which are difficult to obtain by other means. We provide analytical expressions and suggest specific experiments that could be used to determine the dissociation constants.