An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil

AIMS

To evaluate six commercial DNA extraction kits for their ability to isolate PCR-quality DNA from Bacillus spores in various soil samples.

METHODS AND RESULTS

Three soils were inoculated with various amounts of Bacillus cereus spores to simulate an outbreak or intentional release of the threat agent Bacillus anthracis. DNA was isolated from soil samples using six commercial DNA extraction kits. Extraction and purification efficiencies were assessed using a duplex real-time PCR assay that included an internal positive control. The FastDNA(®) SPIN kit for Soil showed the highest DNA extraction yield, while the E.Z.N.A.(®) Soil DNA and PowerSoil(®) DNA Isolation kits showed the highest efficiencies in removing PCR inhibitors from loam soil extracts.

CONCLUSIONS

The results of this study suggest that commercially available extraction kits can be used to extract PCR-quality DNA from bacterial spores in soil. The selection of an appropriate extraction kit should depend on the characteristics of the soil sample and the intended downstream application.

SIGNIFICANCE AND IMPACT OF THE STUDY

  The results of this study aid in the selection of an appropriate DNA extraction kit for a given soil sample. Its application could expedite sample processing for real-time PCR detection of a pathogen in soil.

Reduced ethanol inhibition of N-methyl-D-aspartate receptors by deletion of the NR1 C0 domain or overexpression of alpha-actinin-2 proteins

The depressant actions of ethanol on central nervous system activity appear to be mediated by its actions on a number of important membrane associated ion channels including the N-methyl-d-aspartate (NMDA) subtype of ionotropic glutamate receptor. Although no specific site of action for ethanol on the NMDA receptor has been found, previous studies suggest that the ethanol sensitivity of the receptor may be affected by intracellular C-terminal domains of the receptor that regulate the calcium-dependent inactivation of the receptor. In the present study, co-expression of the NR2A subunit and an NR1 subunit that lacks the alternatively spliced intracellular C1 cassette did not reduce the effects of ethanol on channel function as measured by patch-clamp electrophysiology. Full inhibition was also observed in cells expressing an NR1 subunit truncated at the end of the C0 domain (NR1(863stop)). However, the inhibitory effects of ethanol were reduced by expression of an NR1 C0 domain deletion mutant (NR1(Delta839-863)), truncation mutant (NR1(858stop)), or a triple-point mutant (Arg to Ala, Lys to Ala, and Asn to Ala at 859-861) previously shown to significantly reduce calcium-dependent inactivation. A similar reduction in the effects of ethanol on wild-type NR1/2A but not NR1/2B or NR1/2C receptors was observed after co-expression of full-length or truncated human skeletal muscle alpha-actinin-2 proteins that produce a functional knockout of the C0 domain. The effects of ethanol on hippocampal and cortical NMDA-induced currents were similarly attenuated in low calcium recording conditions, suggesting that a C0 domain-dependent process may confer additional ethanol sensitivity to NMDA receptors.

Fyn tyrosine kinase reduces the ethanol inhibition of recombinant NR1/NR2A but not NR1/NR2B NMDA receptors expressed in HEK 293 cells

NMDA receptors are potentiated by phosphorylation in a subunit- and kinase-specific manner. Both native and recombinant NMDA receptors are inhibited by behaviorally relevant concentrations of ethanol. Whether the phosphorylation state of individual subunits modulates the ethanol sensitivity of these receptors is not known. In this study, the effects of Fyn tyrosine kinase on the ethanol sensitivity of specific recombinant NMDA receptors expressed in HEK 293 cells were investigated. Whole-cell mode patch clamp and ratiometric calcium imaging demonstrated that the degree of ethanol inhibition of NR1/NR2B receptors was unaffected by Fyn tyrosine kinase. In contrast, the inhibition of NR1/NR2A receptors by ethanol (100 mM) was significantly reduced under conditions of enhanced Fyn-mediated tyrosine phosphorylation of the NR2A subunit. This effect was not observed at lower concentrations of ethanol (< or = 50 mM). These results suggest that tyrosine phosphorylation of specific NMDA receptors by Fyn tyrosine kinase may regulate the sensitivity of these receptors to the sedative/hypnotic concentrations of ethanol.

Effects of c-Src tyrosine kinase on ethanol sensitivity of recombinant NMDA receptors expressed in HEK 293 cells

N-Methyl-D-aspartate (NMDA) receptors are ligand-gated ion channels that are important mediators of the actions of the excitatory amino acid neurotransmitter glutamate. Previous studies have shown that ethanol inhibits the function of both wild-type receptors found in neurons and recombinant NMDA receptors expressed in heterologous cells, such as oocytes and transfected mammalian cells. Although some studies have reported that certain subunit combinations display an enhanced sensitivity to ethanol, this effect is not observed in all experimental systems. This discrepancy may be due to varying levels of endogenous modulators, such as kinases, between different cell preparations. In this study, we investigated the effects of tyrosine phosphorylation on the ethanol sensitivity of NMDA receptor function using a recombinant cell system where levels of both NMDA subunits and protein kinases can be more carefully controlled. Human embryonic kidney (HEK 293) cells were transfected with different NMDA receptor subunits and a c-Src-green fluorescent protein (GFP) fusion protein that could be directly visualized in living cells. Agonist-stimulated calcium flux was measured in single cells using fura-2 video imaging. As expected, cells transfected with the NR1/NR2B subunits were more sensitive to inhibition by the NR2 selective antagonist ifenprodil than those transfected with NR1/ NR2A or NR1/NR2A/NR2B subunits. All receptor combinations were inhibited by ethanol (25 and 100 mM), with the NR1/NR2B combination being slightly more sensitive than NR1/NR2A or NR1/NR2A/NR2B. Control and NMDA-receptor transfected HEK 293 cells displayed a low degree of tyrosine phosphorylation as measured by immunofluorescence and Western immunoblotting using an antiphosphotyrosine antibody. Phosphorylation was markedly enhanced in cells transfected with the c-Src-GFP fusion protein. The sensitivity of NMDA receptors to either 25 or 100 mM ethanol, or 10 microM ifenprodil, was not significantly altered by co-transfection with c-Src-GFP. These results indicate that, although NMDA receptors can be a target of c-Src tyrosine kinase, tyrosine phosphorylation by this enzyme does not modulate the inhibitory effects of ethanol on NMDA-activated currents.

Intracellular calcium enhances the ethanol sensitivity of NMDA receptors through an interaction with the C0 domain of the NR1 subunit

Previous studies in this laboratory have shown that the ethanol inhibition of recombinant NMDA receptors expressed in Xenopus oocytes is subunit-dependent, with the NR1/2A receptor being more sensitive than NR1/2C receptors. The ethanol sensitivity of NR1/2A receptors is reduced by substitution of the wild-type NR1-1a (NR1(011)) subunit with the calcium-impermeable NR1 (N616R) subunit. In the present study, the ethanol inhibition of NMDA receptors was determined under different conditions to examine the role that calcium plays in determining the ethanol sensitivity of recombinant NMDA receptors. The ethanol sensitivity of NR1/2B or NR1/2C receptors was not affected by alterations in extracellular calcium levels or by coexpression with calcium-impermeable NR1 mutants. In contrast, the inhibition of NR1/2A receptors by 100 mM ethanol was reduced in divalent-free recording medium and was significantly increased when 10 mM calcium was used as the only charge carrier. The increase in the ethanol sensitivity of NR1/2A receptors under high-calcium conditions was prevented by preinjection of oocytes with the calcium chelator 1,2-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA) but not by inhibitors of calmodulin or protein kinase C. Ethanol did not alter the channel blocking activity of divalent cations on NMDA-induced currents. The enhanced ethanol sensitivity of NR1/2A receptors in 10 mM calcium persisted when the NR1 subunit was replaced by the alternative splice variant NR1-4a (NR1(000)), which lacks the C1 and C2 cassettes. However, expression of a mutant NR1 subunit that lacked the C0, C1, and C2 domains abolished the calcium-dependent enhancement of ethanol's inhibition of NR1/2A receptors. Finally, the ethanol sensitivity of wild-type NR1/2A receptors measured in transfected HEK 293 cells by whole cell patch-clamp electrophysiology was significantly reduced by expression of the C-terminal truncated NR1 subunit. These results demonstrate that the ethanol sensitivity of certain NMDA receptors is modulated by an intracellular, calcium-dependent process that requires the C0 domain of the NR1 subunit.

Site-directed mutagenesis of an amino acid residue in the bacteriophage P2 ogr protein implicated in interaction with Escherichia coli RNA polymerase

The P2 ogr gene encodes a 72-amino-acid protein required for P2 late gene expression. This gene was defined originally by a class of compensatory mutations which overcome the block to P2 late transcription imposed by a host mutation, rpoA109, in the gene encoding the alpha subunit of Escherichia coli RNA polymerase. Spontaneous compensatory ogr mutations substitute a Cys for a Tyr residue at amino acid 42 in the Ogr polypeptide. Using suppression of an ogr amber mutation and site-directed oligonucleotide mutagenesis, we have studied the effect of amino acid substitutions at this position in Ogr. Substitution of charged residues at this site renders Ogr protein inactive, in rpoA+ and rpoA109 strains. While 11 different amino acids are capable of replacing the wild-type Tyr-42 to allow P2 growth to varying degrees in a wild-type E. coli strain, only three of these allow phage growth in strains carrying the rpoA109 mutation. Phages carrying Cys or Ala in place of Tyr-42 gave burst sizes at least as high as P2 ogr+ in a rpoA+ strain; a Gly substitution also allowed P2 to grow in either a rpoA+ or rpoA109 background, but markedly reduced the burst size. These results are consistent with a direct interaction between Ogr and the alpha subunit of E. coli RNA polymerase in positive control of P2 late transcription, and indicate that the block imposed by the rpoA109 mutation is due to steric hindrance.

Deletion analysis of a bacteriophage P2 late promoter

We have fused the promoter (PF) for the P2 late FETUD operon to the gene (cat) encoding chloramphenicol acetyltransferase (CAT) in a plasmid vector. Synthesis of CAT in Escherichia coli strains carrying this plasmid requires the product of the P2 ogr gene or the satellite phage P4 transactivation gene, delta. Our results demonstrate that these phage-encoded transcriptional regulatory proteins are necessary and sufficient for activation of P2 late transcription in this reporter plasmid. Positive regulation of cloned PF is severely impaired in a host strain carrying the rpoA109 mutation. Expression from the cloned promoter thus approximates those features of P2 late transcription that have been shown to occur during normal P2 infection. To define sequences required for promoter function, sequential upstream deletions of PF were generated using BAL 31 nuclease, and the mutant promoters were assayed for cat expression. A sequence between nucleotides -69 and -64 from the transcription start point was found to be essential for promoter activity. This coincides with a region of homology conserved among all four P2 late gene promoters and the two P4 late promoters, and includes an element of dyad symmetry.

Exertional rhabdomyolysis in two prison inmates

We have reported two cases of exertional rhabdomyolysis which resolved without serious complication. The denial and exclusion of significant historical information initially made the specific etiology of rhabdomyolysis indeterminate in the first case.

Lack of recognition of internal medicine as a specialty: a factor in medical student career choice?

Interest among medical students in a career in internal medicine has recently declined. We propose that lack of recognition of general internal medicine as a specialty may be one factor in students' decisions to enter other fields. A survey of 300 first-year and second-year medical students at the Medical College of Georgia showed that 84% of the respondents plan to specialize, yet only 49% recognized general internal medicine as a specialty. Significantly higher percentages of students correctly classified six other specialties. Only family practice was less likely than internal medicine to be recognized as a specialty. Earlier recognition of general internal medicine as a specialty among students who want to specialize might result in an increased number of students entering internal medicine residency programs.