Developing novel species-specific DNA markers for PCR-based species identification of the Lactobacillus sakei group.

Identification of members of the Lactobacillus sakei group (LSG) by common phenotypic and genotypic methods is generally inadequate and time-consuming. The objective of this study was to develop novel species-specific primers based on sequence-characterized amplified region (SCAR) markers using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) analysis. Three species-specific fragments were gel-purified, cloned and sequenced after preliminary screening of 80 random primers. Accordingly, three pairs of primers Lcur-F/R, Lgram-F/R and Lsakei-F/R were designed based on single species-specific bands (281, 278 and 472 bp) that were obtained from Lactobacillus curvatus, Lactobacillus graminis and L. sakei, respectively. The specificities of these primer pairs were confirmed in 21 LSG strains and 31 nontarget Lactobacillus strains. In addition, the detection limits for each primer pair were approx. 105 , 104 and 106 cells per gram of meat samples spiked with L. curvatus, L. graminis and L. sakei, respectively. In conclusion, we have successfully developed a rapid, accurate and effective PCR-based method for identification of species in the LSG. SIGNIFICANCE AND IMPACT OF THE STUDY: Neither phenotypic nor the most commonly used genotypic method (16S rRNA gene sequencing) provides sufficient resolution for accurate identification of the Lactobacillus sakei group. A sequence-characterized amplified region method developed in this study provides a rapid, cost-effective way to detect the member of the L. sakei group in meat sample.

Investigating the biodegradability of perfluorooctanoic acid.

Perfluorooctanoic acid (PFOA) is an industrial chemical that has become disseminated globally in aquatic and terrestrial habitats, humans, and wildlife. Understanding PFOA's biodegradability (susceptibility to microbial metabolic attack) is a crucial element in developing an informed strategy for predicting and managing this compound's environmental fate. Reasoning that PFOA might be susceptible to reductive defluorination by anaerobic microbial communities, we embarked on a 2-phase experimental approach examining the potential of five different microbial communities (from a municipal waste-water treatment plant, industrial site sediment, an agricultural soil, and soils from two fire training areas) to alter PFOA's molecular structure. A series of primarily anaerobic incubations (up to 259d in duration) were established with acetate, lactate, ethanol, and/or hydrogen gas as electron donors and PFOA (at concentrations of 100 ppm and 100 ppb) as the electron acceptor. Cometabolism of PFOA during reductive dechlorination of trichloroethene (TCE) and during reduction of nitrate, iron, sulfate, and methanogenesis were also examined. Endpoints of potential PFOA transformation included release of fluoride and detection of potential transformation products by LC/Orbitrap MS and LC/accurate radioisotope counting in a (14)C radiotracer study. The strongest indication of PFOA transformation occurred during its potential cometabolism at the 100 ppb concentration during reductive dechlorination of TCE. Despite an extensive search for transformation products to corroborate potential cometabolism of PFOA, we were unable to document any alteration of PFOA's chemical structure. We conclude that, under conditions examined, PFOA is microbiologically inert, hence environmentally persistent.

Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment.

Laboratory incubations of coal-tar waste-contaminated sediment microbial communities under relatively controlled physiological conditions were used to interpret results of a field-based stable isotope probing (SIP) assay. Biodegradation activity of 13C-benzene was examined by GC/MS determination of net 13CO2 production and by GC headspace analysis of benzene loss. Key experimental variables were: the site of the assays (laboratory serum-bottle incubations and in situ field sediments), benzene concentration (10, 36 or 200 p.p.m. in laboratory assays), and physiological conditions (anaerobic with or without sulfate or nitrate additions versus aerobic headspace or the uncontrolled field). In anaerobic laboratory incubations of benzene at 10 p.p.m., greater than 60% of the substrate was eliminated within 15 days. During anaerobic incubations of 200 p.p.m. benzene (70 days), 0.9% benzene mineralization occurred. When benzene (36 p.p.m.) was added to sediment with air in the serum-bottle headspace, 14% of the initial 13C was mineralized to 13CO2 in 2.5 days. In the field experiment (178 microg 13C-benzene dosed to undisturbed sediments), net 13CO2 production reached 0.3% within 8.5 h. After isopycnic separation of 13C (heavy)-labelled DNA from the above biodegradation assays, sequencing of 13C-DNA clone libraries revealed a broad diversity of taxa involved in benzene metabolism and distinctive libraries for each biodegradation treatment. Perhaps most importantly, in the field SIP experiment the clone libraries produced were dominated by Pelomonas (betaproteobacteria) sequences similar to those found in the anaerobic 10 p.p.m. benzene laboratory experiment. These data indicate that the physiological conditions that prevail and govern in situ biodegradation of pollutants in the field may be interpreted by knowing the physiological preferences of potentially active populations.

Expressed transcripts associated with high rates of egg production in chicken ovarian follicles.

The purpose of this study was to characterize differentially expressed transcripts associated with varying rates of egg production in Taiwan country chickens. Ovarian follicles were isolated from two strains of chicken which showed low (B) or high (L2) rates of egg production, then processed for RNA extraction and cDNA library construction. Three thousand and eight forty clones were randomly selected from the cDNA library and amplified by PCR, then used in microarray analysis. Differentially expressed transcripts (P<0.05, log(2)> or = 1.75) were sequenced, and aligned using GenBank. This analysis revealed 20 non-redundant sequences which corresponded to known transcripts. Eight transcripts were expressed at a higher level in ovarian tissue prepared from chicken strain B, and 12 transcripts were expressed at a higher level in L2 birds. These differential patterns of expression were confirmed by semi-quantitative RT-PCR. We show that transcripts of cyclin B2 (cycB2), ferritin heavy polypeptide 1 (FTH1), Gag-Pol polyprotein, thymosin beta4 (TB4) and elongation factor 1 alpha1 (EEF1A1) were enriched in B strain ovarian follicles. In contrast, thioredoxin (TXN), acetyl-CoA dehydrogenase long chain (ACADL), inhibitor of growth family member 4 (ING4) and annexin II (ANXA2) were expressed in at higher levels in the L2 strain. We suggest that our approach may lead to the isolation of effective molecular markers that can be used in selection programs in Taiwan country chickens.

The recruitment of Fas-associated death domain/caspase-8 in Ras-induced apoptosis.

Oncogenic Ras induces cells to undergo apoptosis after inhibition of protein kinase C (PKC) activity. The integration of differential signaling pathways is required for full execution of apoptosis. In this study, we used Jurkat as well as Fas/FADD-defective cell lines expressing v-ras to determine the upstream elements required for activation of the caspase cascade in PKC/Ras-mediated apoptosis. During this Ras-induced apoptotic process, caspase-8 was activated, possibly through its binding to Fas-associated death domain (FADD), in Jurkat/ras and Jurkat/Fas(m)/ras cells but not in Jurkat/FADD(m)/ras cells. c-Jun NH(2)-terminal kinase (JNK) was activated in all three cell lines expressing ras in response to apoptotic stimulation. Suppression of JNK by dn-JNK1 blocked the interaction of FADD and caspase-8 and partially protected Jurkat/ras and Jurkat/Fas(m)/ras cells from apoptosis. However, dn-JNK1 had no effect on PKC/Ras-induced apoptosis in Jurkat/FADD(m)/ras cells. The results indicate that FADD/caspase-8 signaling is involved in PKC/Ras-mediated apoptosis, and JNK may be an upstream effector of caspase activation.

Redox control of retinoic acid receptor activity: a novel mechanism for retinoic acid resistance in melanoma cells.

Retinoic acid (RA) slows growth and induces differentiation of tumor cells through activation of RA receptors (RARs). However, melanoma cell lines display highly variable responsiveness to RA, which is a poorly understood phenomenon. By using Northern and Western blot analyses, we show that RA-resistant A375 and RA-responsive S91 melanoma cells express comparable levels of major components of RAR-signaling pathways. However, A375 cells have substantially higher intracellular reactive oxygen species (ROS) levels than S91 cells. Lowering ROS levels in A375 cells through hypoxic culture conditions restores RAR-dependent trans-activity, which could be further enhanced by addition of the antioxidant N-acetyl-cysteine. Hypoxia also enhances RAR activity in the moderately RA-responsive C32 cells, which have intermediate ROS levels. Conversely, increasing oxidative stress in highly RA-responsive S91 and B16 cells, which have low ROS levels, by treatment with H(2)O(2) impairs RAR activity. Consistent with these observations, RA more potently inhibited the proliferation of hypoxic A375 cells than that of normoxic cells. Oxidative states diminish, whereas reducing conditions enhance, DNA binding of retinoid X receptor/RAR heterodimers in vitro, providing a molecular basis for the observed inverse correlation between RAR activity and ROS levels. The redox state of melanoma cells provides a novel, epigenetic control mechanism of RAR activity and RA resistance.

Oncogenic ras mediates apoptosis in response to protein kinase C inhibition through the generation of reactive oxygen species.

Ras is a well established modulator of apoptosis. Suppression of protein kinase C (PKC) activity can selectively induce apoptosis in cells expressing a constitutively activated Ras protein. We wished to determine whether reactive oxygen species serve as an effector of Ras-mediated apoptosis. Ras-transformed NIH/3T3 cells contained higher basal levels of intracellular H(2)O(2) compared with normal NIH/3T3 cells, and PKC inhibition up-regulated ROS to 5-fold greater levels in Ras-transformed cells than in normal cells. Treatment with N-acetyl-l-cysteine reduced both the basal and inducible levels of intracellular H(2)O(2) in NIH/3T3-Ras cells and antagonized the induction of apoptosis by PKC inhibition. Culturing NIH/3T3-Ras cells in low oxygen conditions, which prevents ROS generation, also inhibited the apoptotic response to PKC inhibition. These results suggest that reactive oxygen species are necessary as downstream effectors of the Ras-mediated apoptotic response to PKC inhibition. However, the generation of ROS alone is not sufficient to induce apoptosis in Ras-transformed cells because inhibition of cell cycle progression prevented the induction of apoptosis in NIH/3T3-Ras cells without inhibiting the generation of intracellular H(2)O(2) observed after PKC inhibition. These findings suggest that continued cell cycle progression of Ras-transformed cells during PKC inhibition is also necessary for the induction of apoptosis.

Regulation of NF-kappa B activation in T helper 1 and T helper 2 cells.

In most cell types, NF-kappa B is activated by release from a cytoplasmic inhibitor protein, I kappa B, followed by its translocation to the nucleus where it binds to the regulatory regions of many genes, including the IL-2 gene in T lymphocytes. We have previously shown by electrophoretic mobility shift assays that nuclear extracts prepared from activated, non-IL-2-producing Th2 cell clones. We show here that Th-1 and Th2 cells have similar levels of cytoplasmic p65(RelA) and p50, but TCR stimulation fails to induce the nuclear translocation of p65(RelA) in Th2 cells. Nuclear translocation of p65(RelA) can be induced by IL-1 stimulation of Th2 cells, indicating that a basic mechanism of NF-Kappa B activation common to many cells is intact in Th2 cells. We demonstrate that IL-1 and TNF induce rapid nuclear translocation of p65(RelA) in T cell clones, whereas TCR-induced NF-Kappa B activation in Th1 cells is delayed and may be longer in duration. This suggests that the TCR pathway of NF-Kappa B activation is different from the cytokine pathway. Furthermore, we show that Th1 and Th2 cells express different levels and/or different forms of I kappa B alpha, and that cytokines, but not TCR stimuli, significantly modulate detectable levels of cytoplasmic I kappa B alpha.

Regulation of cytokine gene expression in T helper cell subsets.

We have examined the transcriptional regulation of the Th1-specific IL-2 gene and the Th2-specific IL-4 gene by transient transfection of promoter-chloramphenicol acetyl transferase (CAT) constructs into T cell clones and by electrophoretic mobility shift assays. Transfection of the Th2 clone D10.G4 with IL-4 promoter-CAT constructs demonstrated anti-CD3 inducible IL-4 promoter activity. In contrast, CAT constructs containing murine IL-2 promoter sequences were not inducible in D10.G4 cells. Transfection analyses in the Th1 clone D1.1 demonstrated inducible IL-2 promoter activity but no IL-4 promoter activity. Electrophoretic mobility shift assays using well-defined regulatory elements in the murine IL-2 gene promoter showed that anti-CD3 stimulation of Th2 clones failed to induce a characteristic increase in the ratio of p65-p50:p50-p50 NF-kappa B binding complexes in the nucleus that did occur in IL-2-producing clones. In addition, other protein complexes with NF-kappa B binding sequences were seen using lysates from Th1 and Th0 cells but not Th2 cells. Thus, expression of the promoter-CAT constructs directly correlates with endogenous IL-2 and IL-4 gene expression in Th1 and Th2 clones, confirming that the differential expression of IL-2 and IL-4 genes in these T cells is transcriptionally controlled. Furthermore, the lack of IL-2 transcription in activated Th2 cells is associated with the failure to generate required IL-2 gene promoter binding proteins, particularly NF-kappa B in the nucleus.