Dedicated farnesyl diphosphate synthases circumvent isoprenoid-derived growth-defense tradeoffs in Zea mays.

Zea mays (maize) makes phytoalexins such as sesquiterpenoid zealexins, to combat invading pathogens. Zealexins are produced from farnesyl diphosphate in microgram per gram fresh weight quantities. As farnesyl diphosphate is also a precursor for many compounds essential for plant growth, the question arises as to how Z. mays produces high levels of zealexins without negatively affecting vital plant systems. To examine if specific pools of farnesyl diphosphate are made for zealexin synthesis we made CRISPR/Cas9 knockouts of each of the three farnesyl diphosphate synthases (FPS) in Z. mays and examined the resultant impacts on different farnesyl diphosphate-derived metabolites. We found that FPS3 (GRMZM2G098569) produced most of the farnesyl diphosphate for zealexins, while FPS1 (GRMZM2G168681) made most of the farnesyl diphosphate for the vital respiratory co-factor ubiquinone. Indeed, fps1 mutants had strong developmental phenotypes such as reduced stature and development of chlorosis. The replication and evolution of the fps gene family in Z. mays enabled it to produce dedicated FPSs for developmentally related ubiquinone production (FPS1) or defense-related zealexin production (FPS3). This partitioning of farnesyl diphosphate production between growth and defense could contribute to the ability of Z. mays to produce high levels of phytoalexins without negatively impacting its growth.

Influence of glucocorticoids, neuregulin-1ß, and sex on surfactant phospholipid secretion from type II cells.

Glucocorticoids induce lung fibroblasts to produce fibroblast-pneumocyte factor, a peptide that stimulates type II cells to synthesize pulmonary surfactant. This effect is known to be more apparent in cells derived from female fetuses, a characteristic that has been attributed to sex-linked differences in the fibroblasts. In the current study, it has been shown that dexamethasone enhances both ß-adrenergic receptor (ß-AR) activity (1.3- to 1.6-fold increase) and (-)-isoproterenol-induced secretion of surfactant (1.8- to 1.9-fold increase) in type II cells. However, fibroblast-conditioned media (FCM), prepared in the presence of dexamethasone, generates a much greater response to (-)-isoproterenol (3.1- to 3.8-fold increase). Furthermore, each of these effects is more pronounced if both cell types are female-derived. It is hypothesized that the enhanced response to glucocorticoids is the result of a synergistic effect between the steroid and a component of FCM. Neuregulin-1ß (NRG1ß), which is elevated in FCM generated in the presence of dexamethasone, influences not only the rate of surfactant secretion and the ß-AR activity in type II cells, but also enhances in both sexes the cellular response to (-)-isoproterenol. These results suggest that NRG1ß might be more effective than glucocorticoids in treating prematurely born male infants, which are known to respond poorly to glucocorticoids. Given that glucocorticoids are known to induce higher levels of ß-AR mRNA, the effect of NRG1ß, alone and in combination with dexamethasone, on ß-AR gene expression was measured using qRT-PCR. Whereas NRG1ß had no effect alone, in combination with dexamethasone it produced up to a 4.2-fold elevation in the level of ß-AR mRNA.

A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studies.

BACKGROUND: The frequent recurrence of early-stage non-small-cell lung cancer (NSCLC) is generally attributable to metastatic disease undetected at complete resection. Management of such patients depends on prognostic staging to identify the individuals most likely to have occult disease. We aimed to develop and validate a practical, reliable assay that improves risk stratification compared with conventional staging. METHODS: A 14-gene expression assay that uses quantitative PCR, runs on formalin-fixed paraffin-embedded tissue samples, and differentiates patients with heterogeneous statistical prognoses was developed in a cohort of 361 patients with non-squamous NSCLC resected at the University of California, San Francisco. The assay was then independently validated by the Kaiser Permanente Division of Research in a masked cohort of 433 patients with stage I non-squamous NSCLC resected at Kaiser Permanente Northern California hospitals, and on a cohort of 1006 patients with stage I-III non-squamous NSCLC resected in several leading Chinese cancer centres that are part of the China Clinical Trials Consortium (CCTC). FINDINGS: Kaplan-Meier analysis of the Kaiser validation cohort showed 5 year overall survival of 71·4% (95% CI 60·5-80·0) in low-risk, 58·3% (48·9-66·6) in intermediate-risk, and 49·2% (42·2-55·8) in high-risk patients (p(trend)=0·0003). Similar analysis of the CCTC cohort indicated 5 year overall survivals of 74·1% (66·0-80·6) in low-risk, 57·4% (48·3-65·5) in intermediate-risk, and 44·6% (40·2-48·9) in high-risk patients (p(trend)<0·0001). Multivariate analysis in both cohorts indicated that no standard clinical risk factors could account for, or provide, the prognostic information derived from tumour gene expression. The assay improved prognostic accuracy beyond National Comprehensive Cancer Network criteria for stage I high-risk tumours (p<0·0001), and differentiated low-risk, intermediate-risk, and high-risk patients within all disease stages. INTERPRETATION: Our practical, quantitative-PCR-based assay reliably identified patients with early-stage non-squamous NSCLC at high risk for mortality after surgical resection. FUNDING: UCSF Thoracic Oncology Laboratory and Pinpoint Genomics.

Motor deficit and lack of overt dystonia in Dlx conditional Dyt1 knockout mice.

DYT1 or DYT-TOR1A dystonia is early-onset generalized dystonia caused by a trinucleotide deletion of GAG in the TOR1A or DYT1 gene leads to the loss of a glutamic acid residue in the resulting torsinA protein. A mouse model with overt dystonia is of unique importance to better understand the DYT1 pathophysiology and evaluate preclinical drug efficacy. DYT1 dystonia is likely a network disorder involving multiple brain regions, particularly the basal ganglia. Tor1a conditional knockout in the striatum or cerebral cortex leads to motor deficits, suggesting the importance of corticostriatal connection in the pathogenesis of dystonia. Indeed, corticostriatal long-term depression impairment has been demonstrated in multiple targeted DYT1 mouse models. Pappas and colleagues developed a conditional knockout line (Dlx-CKO) that inactivated Tor1a in the forebrain and surprisingly displayed overt dystonia. We set out to validate whether conditional knockout affecting both cortex and striatum would lead to overt dystonia and whether machine learning-based video behavioral analysis could be used to facilitate high throughput preclinical drug screening. We generated Dlx-CKO mice and found no overt dystonia or motor deficits at 4 months. At 8 months, retesting revealed motor deficits in rotarod, beam walking, grip strength, and hyperactivity in the open field; however, no overt dystonia was visually discernible or through the machine learning-based video analysis. Consistent with other targeted DYT1 mouse models, we observed age-dependent deficits in the beam walking test, which is likely a better motor behavioral test for preclinical drug testing but more labor-intensive when overt dystonia is absent.

Lack of Seed Coat Contamination with Cucumber mosaic virus in Lupin Permits Reliable, Large-Scale Detection of Seed Transmission in Seed Samples.

Sowing seed stocks with minimal virus content provides a key control measure in preventing damaging epidemics of Cucumber mosaic virus (CMV) in crops of narrow-leafed lupin (Lupinus angustifolius). A seed testing service provides an estimate of percent CMV infection based on a dry seed test in which bulked subsamples of ungerminated seed are ground to a fine powder for testing. When enzyme-linked immunosorbent assay (ELISA) was used, CMV antiserum that gave low background optical density (A405) values with extracts of powder from subsamples of healthy seed provided greatest accuracy, readily detecting one infected seed in subsamples of 100 seeds. In comparative ELISAs on duplicate subsamples from eight different seed stocks, germination and dry seed tests always gave similar percent infection values. When seed coats were separated from the embryos of CMV-infected and healthy lupin seeds before testing by ELISA, the virus was only detected in embryos from infected seeds and never in their seed coats. Treatment with trisodium phosphate did not alter the low ELISA optical density (A405) values obtained with seed coats separated from infected seeds. Therefore, seed coat contamination with CMV is lacking in lupin, justifying large-scale routine use of a dry seed test to estimate percent virus infection in commercial seed samples.

A fluorescent based PCR assay for the detection and quantitation of Giardia duodenalis genotypes in mixed populations.

A method based on the polymerase chain reaction has been developed for differentiating between genotypically and phenotypically distinct strains of Giardia duodenalis and quantifying the amount of initial template of the different genotypes in mixed populations. The assay relies on a sequence-specific probe, labelled with two fluorescent dyes, designed to bind within the small subunit ribosomal (SSU) RNA gene. This target region is amplified by primers specific for either Group 1 or Group 2-type isolates of G. duodenalis and the probe binds within the primer-targeted region. This quantitative method takes advantage of the 5' nuclease activity of Taq DNA polymerase, which, on encountering a probe bound within the target DNA sequence cleaves it, causing it to become dissociated from the template. When the two fluorescent dyes bound to the probe are in close proximity (when the probe is intact), the interaction of the two dyes prevents the reporter dye from fluorescing. However, during the extension phase of amplification, the activity of the DNA polymerase causes the dyes to become separated and hence the reporter dye increases its fluorescent intensity. This release of fluorescence is directly related to the amplified amount of target template. This assay was developed with the aim of providing a unique method with which to investigate interactions within mixed populations of genetically distinct strains of G. duodenalis.

Liquid chromatographic-tandem mass spectrometric determination of nonylphenol polyethoxylates and nonylphenol carboxylic acids in surface water.

This paper presents a new LC-MS-MS method for the determination of the concentration of nonylphenol ethoxylates (NPEOs) and nonylphenol carboxylic acids (NPECs) in surface and drinking water using a reversed-phase column, which is fast and specific by nature. This method allows the simultaneous analysis of the two families of compounds in the same extract. Liquid-solid extraction of 100 ml of sample is performed on graphitized carbon black (GCB) cartridges. Reversed-phase chromatography is performed on a C8 column with isocratic elution. The electrospray interface is used to monitor the [M+NH4]+ ion for NPEOs and the [M-H]- ion for NPECs. Detection limits range from 0.01 to 0.05 microg/l for NP(1-17)EOs and are 0.01 microg/l for NP(1-2)ECs. Mean recoveries range from 78 to 107% with relative standard deviations ranging from 6 to 16%. Applicability of the method is demonstrated by results from a monthly sampling of river water at 11 sampling points located downstream of suspected polluting industries in Quebec (Canada).

Nonylphenolic compounds in drinking and surface waters downstream of treated textile and pulp and paper effluents: a survey and preliminary assessment of their potential effects on public health and aquatic life.

Eleven drinking water treatment plants, located downstream of textile plants or pulp and paper mills, have been sampled monthly during a year for the analysis of 17 nonylphenol ethoxylates (NP1-17EO) and two nonylphenoxycarboxylic acids (NP1-2EC). At all but one plant, results in the drinking water, for the sum of these 19 substances, range between below detection levels and 6.7 microg/l. Annual means are between 0.02 and 2.8 microg/l. At the other plant, the yearly average concentration is 10.4 microg/l and the monthly maximum is 43.3 microg/l. In the surface (pre-treatment) water, the annual mean concentrations of the 11 plants range between 0.14 and 17.8 microg/l and the recorded instantaneous maximum is 55.3 microg/l. According to Canadian health authorities, drinking water is a negligible route of human exposure to nonylphenolic compounds, even at the highest concentrations found in this study. After transformation of the data into nonylphenol equivalents, about 20% of the surface water samples exceed the Canadian 1 microg/l nonylphenol water quality guideline for the protection of aquatic life. Some results also exceed Québec's 6 microg/l nonylphenol guideline. The efficiency of the plants in removing nonylphenolic compounds from drinking water is highly variable, ranging from 11% to 99%.

Novel brominated flame retardants and dechloranes in three fish species from the St. Lawrence River, Canada.

Restrictions in the utilization of polybrominated diphenyl ether (PBDE) mixtures have led to the increased usage of alternative flame retardant additives in a wide range of commercial applications. The present study examined the occurrence of established and emerging flame retardants (FRs) in fish from a densely-populated urbanized sector of the St. Lawrence River (Montreal, Quebec, Canada). Thirty-eight PBDE congeners and sixteen emerging FRs were determined in fish belonging to three predatory species (yellow perch, northern pike, and muskellunge). The ∑PBDE in fish were up to 24,115 ng/g lipid weight (l.w.) in the apex predator muskellunge. Twelve emerging FRs including bis(2-ethylhexyl)-tetrabromophthalate (BEHTBP), pentabromoethylbenzene (PBEB), Dechlorane Plus (anti and syn), dechloranes (Dec) 602, Dec 604, Dec 604 Compound B (Dec 604 CB), and Chlordene Plus (CP) were detected (>0.01 ng/gl.w.) in the liver of muskellunge and northern pike but not in yellow perch homogenates. This is the first report of Dec 604 CB in any fish species. The bioavailability of these FRs in human-impacted aquatic ecosystems warrants further environmental assessment and toxicity testing.

Role of neuregulin-1ß in dexamethasone-enhanced surfactant synthesis in fetal type II cells.

It is well established that glucocorticoids elevate the production of fibroblast-pneumocyte factor (FPF), which induces type II cells to synthesize surfactant phospholipids. FPF, however, has not been identified and it is not clear whether it is a single factor or a complex mixture of factors. In this study it has been shown that, when lung fibroblasts are exposed to dexamethasone, the concentration of neuregulin-1ß (NRG1ß) in conditioned medium is elevated 2-fold (P<0.05), even though NRG1ß gene expression is unaffected. This, together with the finding that exposure of type II cells to NRG1ß directly stimulates by 3-fold the rate of phospholipid synthesis (P<0.05), suggests that NRG1ß is a component of FPF that promotes lung development.

Analytical validation of a practical molecular assay prognostic of survival in nonsquamous non-small cell lung cancer.

A molecular assay prognostic of survival in resected nonsquamous non-small cell lung cancer designed to meet the need for improved risk stratification in early-stage disease has recently been described. This assay measures the expression levels of 14 genes using RNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues. The assay underwent blinded clinical validation in 2 large international cohorts involving approximately 1500 patients; the analytical precision and reproducibility of this assay, however, have not yet been reported. For each of the 14 TaqMan quantitative polymerase chain reaction (PCR) primer and probe sets used in the molecular prognostic assay, the linear range, PCR efficiency, limits of blank, limits of quantitation, and quantitative bias were determined using serial dilutions of pooled RNA extracted from FFPE samples. The reproducibility of the entire molecular assay was determined by performing repeat testing of FFPE samples over multiple days. The linear range of individual quantitative TaqMan PCR primer and probe sets was between 2(10)- and 2(15)-fold input RNA. The median C(T) of the quantitative PCR primer and probe sets at 10 ng of input RNA was 24.3; the median efficiency was 91.2%. The median quantitative bias across all quantitative PCR primer and probe sets was 0.75% (range, 0.32% to 1.32%). In repeat testing, the mean SD of the risk score (scaled from 1 to 100) was 2.18, with a mean coefficient of variation of 0.08. The molecular prognostic assay presented in this study demonstrates high precision and reproducibility, validating its clinical utility as a reliable prognostic tool that can contribute to the management of patients with early-stage disease.