Astrocytic connectivity in the hippocampus

Little is known about the functional connectivity between astrocytes in the CNS. To explore this issue we photo-released glutamate onto a single astrocyte in murine hippocampal slices and imaged calcium responses. Photo-release of glutamate causes a metabotropic glutamate receptor (mGluR)-dependent increase in internal calcium in the stimulated astrocyte and delayed calcium elevations in neighboring cells. The delayed elevation in calcium was not caused by either neuronal activity following synaptic transmission or by glutamate released from astrocytes. However, it was reduced by flufenamic acid (FFA), which is consistent with a role for adenosine triphosphate (ATP) release from astrocytes as an intercellular messenger. Exogenous ligands such as ATP (1 mircoM) increased the number of astrocytes that were recruited into coupled astrocytic networks, indicating that extracellular accumulation of neurotransmitters modulates neuronal excitability, synaptic transmission and functional coupling between astrocytes.     

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

DNA extraction bias is a frequently cited but poorly understood limitation of molecular characterizations of environmental microbial communities. To assess the bias of a commonly used soil DNA extraction kit, we varied the cell lysis protocol and conducted multiple extractions on subsamples of clay, sand, and organic soils. DNA, as well as bacterial and fungal ribosomal gene copies as measured by quantitative PCR, continued to be isolated in successive extractions. When terminal restriction fragment length polymorphism was used, a significant shift in community composition due to extraction bias was detected for bacteria but not for fungi. Pyrosequencing indicated that the relative abundances of sequences from rarely cultivated groups such as Acidobacteria, Gemmatimonades, and Verrucomicrobia were higher in the first extraction than in the sixth but that the reverse was true for Proteobacteria and Actinobacteria. This suggests that the well-known phylum-level bacterial cultivation bias may be partially exaggerated by DNA extraction bias. We conclude that bias can be adequately reduced in many situations by pooling three successive extractions, and additional measures should be considered when divergent soil types are compared or when comprehensive community analysis is necessary.The vast majority of soil bacteria (1, 7, 27) and fungi (13, 29) cannot be cultured via traditional laboratory techniques and must be identified using molecular methods. Successful characterization of microbial communities is therefore often dependent on DNA that is extracted from the environment. However, extraction of high-quality DNA from soil can be problematic (8, 11, 22, 26). Commercial DNA extraction kits are now commonly used in the assessment of taxonomic and functional diversity, community composition, and population abundance (e.g., references 19, 21, 23, 25, and 31). Studies comparing various kits (18, 32) or comparing commercial kits to other methods (2, 10, 24) have shown that DNA yield and purity vary depending on methodology and soil type. While these comparative studies are valuable, it is still unclear to what extent these protocols yield genomic DNA representative of the microbial community found within soil.Our objective in this study was to optimize and assess the bias of a widely used commercial soil DNA extraction kit. We hypothesized that cell lysis would be enhanced and DNA would be removed from adsorption sites by conducting multiple extractions on a single sample, thereby increasing genomic DNA yield and obtaining a more complete survey of microbial taxa. This hypothesis was tested by (i) varying the extraction protocol and measuring DNA yield for three soils with differing characteristics and (ii) examining extraction bias in the genomic DNA obtained from successive extractions by using an improved method. Analytical replicates rather than biological replicates were used in order to focus strictly on variation and bias introduced through methodology, although multiple soil types were analyzed to determine whether biases detected were consistent.     

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

Stable isotope probing with [¹³C]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [¹³C]DNA after a 14-day incubation with [¹³C]biphenyl revealed the dominant organisms to be members of the genera Achromobacter and Pseudomonas. A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [¹³C]DNA fraction revealed two sequence groups similar to bphA (encoding biphenyl dioxygenase) of Comamonas testosteroni strain B-356 and of Rhodococcus sp. RHA1. A library of 1,568 cosmid clones was produced from the [¹³C]DNA fraction. A 31.8-kb cosmid clone, detected by aromatic dioxygenase primers, contained genes of biphenyl dioxygenase subunits bphAE, while the rest of the clone''s sequence was similar to that of an unknown member of the Gammaproteobacteria. A discrepancy in G+C content near the bphAE genes implies their recent acquisition, possibly by horizontal transfer. The biphenyl dioxygenase from the cosmid clone oxidized biphenyl and unsubstituted and para-only-substituted rings of polychlorinated biphenyl (PCB) congeners. A DNA-stable isotope probing-based cosmid library enabled the retrieval of functional genes from an uncultivated organism capable of PCB metabolism and suggest dispersed dioxygenase gene organization in nature.Commercially used polychlorinated biphenyls (PCBs), which are mixtures of more than 60 individual chlorinated biphenyl congeners, are among the most persistent anthropogenic chemical pollutants that threaten natural ecosystems and human health (1). Numerous biphenyl-degrading microorganisms have been isolated and studied, especially for the range of PCB congeners that they degrade. Research has been primarily focused on the biodegradative pathways and the biphenyl dioxygenases responsible for initial PCB oxidation by isolated bacteria (14, 27). Knowledge, however, is limited concerning the indigenous microbial populations that metabolize PCBs in the environment. Stable isotope probing (SIP) coupled with metagenomics is one approach to more directly explore which organisms and genetic information may be involved in PCB degradation in PCB-contaminated sites.SIP was developed to separate and concentrate the nucleic acids or fatty acids of microbial populations that metabolize and, hence, assimilate the isotopically labeled substrates into new cell material (4, 5, 28). Recently, the active PCB degraders in a biofilm community on PCB droplets were revealed as Burkholderia species by using DNA-SIP (32). In another DNA-SIP study, 75 different genera that acquired carbon from [¹³C]biphenyl were found in the PCB-contaminated root zone of a pine tree (22). In addition, that heavy [¹³C]DNA fraction revealed new dioxygenase sequences and possible PCB degradation pathways from GeoChip (16) results and from PCR-amplified sequences obtained by using primers targeting aromatic-ring-hydroxylating dioxygenase (ARHD) genes (22).A major hurdle in using DNA-SIP for metagenomic analyses (9) is the very small amount of heavy DNA that is produced and, hence, recovered, making library construction difficult. Two studies have shown the feasibility of DNA-SIP for metagenomic analyses for C-1 compound-utilizing communities, but they first increased the amount of the heavy DNA fraction by multiple-displacement amplification (6, 10) or enriched the community by growth in sediment slurries. (18).In this study, we used [¹³C]biphenyl to probe for potential PCB-degrading populations in a PCB-contaminated river sediment and to recover genes potentially involved in the critical first step of PCB degradation, the dioxygenase attack. We found a 31.8-kb cosmid clone that contained a biphenyl dioxygenase sequence (bphAE) and demonstrated its activity on PCBs.     

Extremely low-frequency magnetic fields modulate nitric oxide signaling in rat brain

Our previous study has shown that an extremely low‐frequency magnetic field (ELF‐MF) induces nitric oxide (NO) synthesis by Ca²⁺‐dependent NO synthase (NOS) in rat brain. The present study was designed to confirm that ELF‐MF affects neuronal NOS (nNOS) in several brain regions and to investigate the correlation between NO and nNOS activation. The exposure of rats to a 2 mT, 60 Hz ELF‐MF for 5 days resulted in increases of NO levels in parallel with cGMP elevations in the cerebral cortex, striatum, and hippocampus. Cresyl violet staining and electron microscopic evaluation revealed that there were no significant differences in the morphology and number of neurons in the cerebral cortex, striatum, and hippocampus. Differently, the numbers of nNOS‐immunoreactive (IR) neurons were significantly increased in those cerebral areas in ELF‐MF‐exposed rats. These data suggest that the increase in NO could be due to the increased expression and activation of nNOS in cells. Based on NO signaling in physiological and pathological states, ELF‐MF created by electric power systems may induce various physiological changes in modern life. Bioelectromagnetics 33:568–574, 2012. © 2012 Wiley Periodicals, Inc.     

Rapid identification of Lactobacillus and Bifidobacterium in probiotic products using multiplex PCR

Lactic acid bacteria (LAB) are beneficial for the gastrointestinal tract and reinforce immunity in human health. Recently, many functional products using the lactic acid bacteria have been developed. Among these LAB, Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum are frequently used for probiotic products. In order to monitor these LAB in commercial probiotic products, a multiplex PCR method was developed. We designed four species-specific primer pairs for multiplex PCR from the 16S rRNA, 16S-23S rRNA intergenic spacer region, and 23S rRNA genes in Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum. Using these primer pairs, 4 different LAB were detected with high specificity in functional foods. We suggest that the multiplex PCR method developed in this study would be an efficient tool for simple, rapid, and reliable identification of LAB used as probiotic strains.     

Ectodomain shedding of preadipocyte factor 1 (Pref-1) by tumor necrosis factor alpha converting enzyme (TACE) and inhibition of adipocyte differentiation

Preadipocyte factor 1 (Pref-1), an epidermal growth factor repeat containing transmembrane protein found in the preadipocytes, inhibits adipocyte differentiation in vitro and in vivo. Here, we examined the processing of membrane form of Pref-1A to release the 50-kDa soluble form that inhibits adipocyte differentiation. The ectodomain cleavage of Pref-1 is markedly enhanced by phorbol 12-myristate 13-acetate in a dose- and time-dependent manner. The basal and stimulated cleavage is inhibited by the broad metalloproteinase inhibitor GM6001, a fact that suggests that cleavage of membrane Pref-1A is dependent on a metalloproteinase. Next, we showed that release of soluble Pref-1A is inhibited by TAPI-0 and by a tissue inhibitor of metalloproteinase-3, TIMP-3, that can inhibit tumor necrosis factor alpha converting enzyme (TACE), but not by TIMP-1 or TIMP-2. On the other hand, overexpression of TACE increases Pref-1 cleavage to produce the 50-kDa soluble form. Furthermore, this cleavage was not detected in cells with TACE mutation or with TACE small interfering RNA. TACE-mediated shedding of Pref-1 ectodomain inhibits adipocyte differentiation of 3T3-L1 cells and in Pref-1-null mouse embryo fibroblasts transduced with Pref-1A. Identification of TACE as the major protease responsible for conversion of membrane-bound Pref-1 to the biologically active diffusible form provides a new insight into Pref-1 function in adipocyte differentiation.