Detection of clinically significant mutations in the epidermal growth factor receptor missed by direct sequencing using a highly sensitive DNA endonuclease

10054

Background: Mutations in the epidermal growth factor receptor (EGFR) are associated with sensitivity and resistance to EGFR inhibitors gefitinib and erlotinib in patients with non-small cell lung carcinoma (NSCLC). Direct sequencing is currently used for mutation detection but sensitivity is limited and requires dissection to obtain a relatively pure population of tumor cells. We examined a DNA endonuclease, SURVEYOR, which cleaves mismatched heteroduplexed DNA, as a more sensitive method for EGFR mutation screening and compared it to direct sequencing. Methods: EGFR exons 18–21 from tumor DNA were amplified using PCR, digested with SURVEYOR, and the products analyzed by HPLC. Specimens that produced digestion products were re-analyzed by size separation or by denaturing HPLC followed by fractionation and sequencing. Tumor specimens from 191 NSCLC patients were analyzed: 61 frozen tumors specimens; 91 dissected formalin fixed paraffin embedded (FFPE) and 39 un-dissected FFPE tumor specimens from patients treated with gefitinib or erlotinib in whom clinical outcome was available. 173 specimens were independently analyzed by direct sequencing. Results: We detected 48 EGFR mutations by sequencing and 61 using SURVEYOR. All EGFR mutations identified by sequencing, including those using un-dissected tumor specimens, were detected by SURVEYOR and none were missed (sensitivity: 100%, negative predictive value: 100%). 13 mutations were detected by SURVEYOR not detected by sequencing. This included 5 mutations (4 exon 19 deletions; 1 L858R) in 7 (71%) patients who clinically had a PR to gefitinib or erlotinib but who were wild type by sequencing. In 4 patients, 2 with clinical acquired resistance to gefitinib, a T790M mutation was found which was undetected by sequencing. Conclusions: SURVEYOR analysis is a more sensitive method for EGFR mutation detection than direct sequencing. It can be used to detect EGFR mutations from un-dissected tumor specimens and can detect clinically significant activating or resistance associated EGFR mutations not detected by direct sequencing.

[Table: see text]

Enhanced degradation of waste grass clippings in one and two stage anaerobic systems

The present work investigated the use of a simple rumen-fluid-inoculated anaerobic treatment system for the degradation of organic waste. Fresh rumen fluid collected from a fistulated sheep was used as the inoculum and fresh grass clippings were used as the waste material for treatment. Studies were carried out on both a one-stage system where the ligno-cellulosic fraction breaks down into a mixture of soluble products including volatile fatty acids and a two- stage system where these products are subsequently mineralised to biogas. In the one stage system about 70% of the organic waste was solubilized and in the two stage system about 60% waste material was solubilized in a week. About 50% of the degradation was achieved in a 4 day period, showing that a 4 day solids retention time would be a suitable operating regime. The maximum volatile fatty acid production rate was 327 mg COD l(-1) h(-1). A higher loading rate of 30 g l(-1) d(-1) was achieved in these systems compared to anaerobic digesters. Microbiological studies showed an increase in the number of fungal spores as well as a decrease in the number of protozoa in the treatment system. These numbers attained stable values over the duration of the experiments. The system developed is superior to conventional composting or anaerobic digestion and can be applied for the treatment of ligno-cellulosic agricultural residues.

Two-nucleon momentum distributions measured in 3He(e,e'pp)n

We have measured the 3He(e,e'pp)n reaction at 2.2 GeV over a wide kinematic range. The kinetic energy distribution for "fast" nucleons (p>250 MeV/c) peaks where two nucleons each have 20% or less, and the third nucleon has most of the transferred energy. These fast pp and pn pairs are back to back with little momentum along the three-momentum transfer, indicating that they are spectators. Calculations by Sargsian and by Laget also indicate that we have measured distorted two-nucleon momentum distributions by striking one nucleon and detecting the spectator correlated pair.

Observation of an exotic S = +1 baryon in exclusive photoproduction from the deuteron

In an exclusive measurement of the reaction gammad-->K(+)K(-)pn, a narrow peak that can be attributed to an exotic baryon with strangeness S=+1 is seen in the K(+)n invariant mass spectrum. The peak is at 1.542+/-0.005 GeV/c(2) with a measured width of 0.021 GeV/c(2) FWHM, which is largely determined by experimental mass resolution. The statistical significance of the peak is (5.2+/-0.6)sigma. The mass and width of the observed peak are consistent with recent reports of a narrow S=+1 baryon by other experimental groups.

Measurement of the proton spin structure function g1(x,Q2) for Q2 from 0.15 to 1.6 GeV2 with CLAS

Double-polarization asymmetries for inclusive ep scattering were measured at Jefferson Lab using 2.6 and 4.3 GeV longitudinally polarized electrons incident on a longitudinally polarized NH3 target in the CLAS detector. The polarized structure function g(1)(x,Q2) was extracted throughout the nucleon resonance region and into the deep inelastic regime, for Q(2)=0.15-1.64 GeV2. The contributions to the first moment Gamma(1)(Q2)= integral g(1)(x,Q2) dx were determined up to Q(2)=1.2 GeV2. Using a parametrization for g(1) in the unmeasured low x regions, the complete first moment was estimated over this Q2 region. A rapid change in Gamma(1) is observed for Q2<1 GeV2, with a sign change near Q(2)=0.3 GeV2, indicating dominant contributions from the resonance region. At Q(2)=1.2 GeV2 our data are below the perturbative QCD evolved scaling value.

Measurement of ep-->e' ppi+ pi- and baryon resonance analysis

The cross section for the reaction ep-->e(')ppi(+)pi(-) was measured in the resonance region for 1.4<W<2.1 GeV and 0.5<Q2<1.5 GeV(2)/c(2) using the CLAS detector at Jefferson Laboratory. The data show resonant structures not visible in previous experiments. The comparison of our data to a phenomenological prediction using available information on N(*) and Delta states shows an evident discrepancy. A better description of the data is obtained either by a sizable change of the properties of the P13(1720) resonance or by introducing a new baryon state, not reported in published analyses.

First measurement of transferred polarization in the exclusive ep-->e'K+Lambda--> reaction

The first measurements of the transferred polarization for the exclusive e-->p-->e(')K+Lambda--> reaction have been performed at Jefferson Laboratory using the CLAS spectrometer. A 2.567 GeV beam was used to measure the hyperon polarization over Q2 from 0.3 to 1.5 (GeV/c)(2), W from 1.6 to 2.15 GeV, and over the full K+ center-of-mass angular range. Comparison with predictions of hadrodynamic models indicates strong sensitivity to the underlying resonance contributions. A nonrelativistic quark-model interpretation of our data suggests that the ssmacr; quark pair is produced with spins predominantly antialigned. Implications for the validity of the most widely used quark-pair creation operator are discussed.

Photoproduction of the omega meson on the proton at large momentum transfer

The differential cross section, dsigma/dt, for omega meson exclusive photoproduction on the proton above the resonance region (2.6<W<2.9 GeV) was measured up to a momentum transfer -t=5 GeV2 using the CLAS detector at Jefferson Laboratory. The omega channel was identified by detecting a proton and pi(+) in the final state and using the missing mass technique. While the low momentum transfer region shows the typical diffractive pattern expected from Pomeron and Reggeon exchange, at large -t the differential cross section has a flat behavior. This feature can be explained by introducing quark interchange processes in addition to the QCD-inspired two-gluon exchange.

Influence of co-substrates on structure of microbial aggregates in long-chain fatty acid-fed anaerobic digesters

AIMS

The purpose of this study was to investigate the influence of co-substrates, such as glucose and cysteine, on the structure of microbial aggregates in anaerobic digesters treating oleate, a long-chain fatty acid (LCFA).

METHODS AND RESULTS

Transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM) were used to examine the structure of microbial aggregates. Fluorescence in situ hybridization (FISH) techniques were also used to characterize and localize the different trophic groups present in the aggregates. Oleate was found to inhibit the methanogenic activity and formation of granular biomass in digesters. The addition of co-substrates, such as glucose and cysteine either singly or in combination, increased the methanogenic activity and formation of granular biomass. Glucose was more effective than cysteine in reducing the inhibition by oleate on the methanogenic bacteria and in enhancing the formation of granules.

CONCLUSIONS

The addition of nutrient substrate, such as glucose and cysteine could decrease the toxicity of LCFA on anaerobic granulation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that the addition of other substrates might decrease the toxicity of LCFA on the granulation of biomass in anaerobic digesters and enhance methanogenic activity. A combination of TEM, CLSM and FISH techniques provides a better tool for visualizing microbial aggregates and for differentiating and localizing different microbial groups within these aggregates.

Eta photoproduction on the proton for photon energies from 0.75 to 1.95 GeV

Differential cross sections for gammap-->etap have been measured with tagged real photons for incident photon energies from 0.75 to 1.95 GeV. Mesons were identified by missing mass reconstruction using kinematical information for protons scattered in the production process. The data provide the first extensive angular distribution measurements for the process above W=1.75 GeV. Comparison with preliminary results from a constituent quark model support the suggestion that a third S11 resonance with mass approximately 1.8 GeV couples to the etaN channel.

Q2 Dependence of quadrupole strength in the gamma*p --> Delta(+)(1232) --> p pi(0) transition

Models of baryon structure predict a small quadrupole deformation of the nucleon due to residual tensor forces between quarks or distortions from the pion cloud. Sensitivity to quark versus pion degrees of freedom occurs through the Q2 dependence of the magnetic (M1+), electric (E1+), and scalar (S1+) multipoles in the gamma*p-->Delta(+)-->p pi(0) transition. We report new experimental values for the ratios E(1+)/M(1+) and S(1+)/M(1+) over the range Q2 = 0.4-1.8 GeV2, extracted from precision p(e,e(')p)pi(0) data using a truncated multipole expansion. Results are best described by recent unitary models in which the pion cloud plays a dominant role.

First measurement of the double spin asymmetry in (-->)e(-->)p-->e(prime)pi(+)n in the resonance region

The double spin asymmetry in the (-->)e(-->)p --> e(prime)pi(+)n reaction has been measured for the first time in the resonance region for four-momentum transfer Q2 = 0.35-1.5 GeV(2). Data were taken at Jefferson Lab with the CLAS detector using a 2.6 GeV polarized electron beam incident on a polarized solid NH3 target. Comparison with predictions of phenomenological models shows strong sensitivity to resonance contributions. Helicity-1/2 transitions are found to be dominant in the second and third resonance regions. The measured asymmetry is consistent with a faster rise with Q(2) of the helicity asymmetry A1 for the F(15)(1680) resonance than expected from the analysis of the unpolarized data.

Targeted disruption of the murine Fanconi anemia gene, Fancg/Xrcc9

Fanconi anemia (FA) is a human autosomal recessive cancer susceptibility disorder characterized by cellular sensitivity to mitomycin C and ionizing radiation. Six FA genes (corresponding to subtypes A, C, D2, E, F, and G) have been cloned, and the encoded FA proteins interact in a common cellular pathway. To further understand the in vivo role of one of these human genes (FANCG), we generated a targeted disruption of murine Fancg and bred mice homozygous for the targeted allele. Similar to the phenotype of the previously described Fancc(-/-) and Fanca(-/-) mice, the Fancg(-/-) mice had normal viability and no gross developmental abnormalities. Primary splenic lymphocytes, bone marrow progenitor cells, and murine embryo fibroblasts from the Fancg(-/-) mice demonstrated spontaneous chromosome breakage and increased sensitivity to mitomycin C and, to a lesser extent, ionizing radiation. Fancg(-/-) lymphocytes had a defect in the FA pathway, based on their failure to activate the monoubiquitination of the downstream Fancd2 protein in response to IR. Finally, Fancg(-/-) mice had decreased fertility and abnormal gonadal histology. In conclusion, disruption of the Fancg gene confirms the role of Fancg in the FA pathway. The Fancg(-/-) mouse may be useful as an animal model for future gene therapy and cancer susceptibility studies.

Rich dynamics of a ratio-dependent one-prey two-predators model

The objective of this paper is to systematically study the qualitative properties of a ratio-dependent one-prey two-predator model. We show that the dynamics outcome of the interactions are very sensitive to parameter values and initial data. Specifically, we show the interactions can lead to all the following possible outcomes: 1). competitive exclusion; 2). total extinction, i.e., collapse of the whole system; 3). coexistence in the form of positive steady state; 4). coexistence in the form of oscillatory solutions; and 5). introducing a friendly and better competitor can save a otherwise doomed prey species. These results reveal far richer dynamics compared to similar prey dependent models. Biological implications of these results are discussed.

[Historical and herbalogical studies on coloring crude drug (Part 1): "Langbacao"]

The name of Langbacao was described for the first time in Kai Bao Ben Cao in 10th century, in which Langbacao was introduced as an herb medicine for scours. While, as the name of Qu, Wujie, it was first described in Er Ya and as the name of Langyecao, it was first described in Ben Cao Shi Yi. Many investigators have confirmed that the original plant of Langbacao is to be Bidens tripartita L. In Japan, Langbacao is generally recognized as ta-u-ko-gi, while some investigators suggested that it is unlikely that ta-u-ko-gi is identical to Langbacao. In the old Chinese literature, Langbacao had been mentioned as a dye which could make hair dark. But in modern Chinese and Japanese literature, few papers reported the use of Bidens tripartita L. as a dye. The characteristics of the shapes of Langbacao between old and modern literature seem not to be consistent. Other names of Langbacao are confused even in the modern literature. It seems that Langbacao in the old literature includes species of the genus Bidens other than B. tripartita.

Photoproduction of the rho(0) meson on the proton at large momentum transfer

The differential cross section, d sigma/dt, for rho(0) meson photoproduction on the proton above the resonance region was measured up to a momentum transfer -t = 5 GeV2 using the CLAS detector at the Thomas Jefferson National Accelerator Facility. The rho(0) channel was extracted from the measured two charged-pion cross sections by fitting the pi(+)pi(-) and p pi(+) invariant masses. The low momentum transfer region shows the typical diffractive pattern expected from Reggeon exchange. The flatter behavior at large -t cannot be explained solely in terms of QCD-inspired two-gluon exchange models. The data indicate that other processes, like quark interchange, are important to fully describe rho photoproduction.

Moderate hypothermia therapy for patients with severe head injury

OBJECTIVE

To evaluate the effect and safety of early moderate hypothermia therapy (MHT) on patients with head injury by using parallel-control test.

METHODS

Thirty patients with severe head injury within 6 hours after accidents were treated by MHT generally for 4-10 days. The other 30 patients with similar head injury treated routinely were enrolled for a parallel-control test. The mortality, morbidity and changes of some neuro-functional indexes as Glasgow Coma Scores, and Glasgow Outcome Scale, levels of endothelin and some other factors of neurobiochemistry in blood plasma were observed. Meanwhile, the dynamic monitoring by transcranial Doppler ultrasonography was conducted in these patients.

RESULTS

The mortality in MHT group was significantly lower than that in control group. MHT not only reduced endothelin but also increased the brain biochemical factors, which were helpful to the protection of neurons in the early brain ischemia after head injury.

CONCLUSIONS

Early MHT can help reduce mortality and morbidity in patients with acute head injury.

High concentrations of adrenergic antagonists prolong sciatic nerve blockade by tetrodotoxin

BACKGROUND

Millimolar-range concentrations of some adrenergic antagonists have been shown to have local anesthetic-like properties, and to stimulate GTPase activity in vitro. In this report, we investigate whether these agents can potentiate the effect of tetrodotoxin (TTX) and bupivacaine, a conventional local anesthetic, and whether GTPase activation plays a role.

METHODS

Rats received sciatic nerve blockade with tetrodotoxin or bupivacaine co-injected with adrenergic antagonists and/or agonists, or pertussis toxin. Thermal nociceptive blockade was quantified with modified hotplate testing.

RESULTS

Nerve block from TTX alone lasted 153 (99-223) min (median and 25th and 75th percentiles). Co-injection with 20 mM phentolamine, propranolol, and yohimbine prolonged TTX block to 856 (765-862), 486 (444-510), and 465 (413-495) min respectively (P<0.005 in all cases, compared to TTX alone). Micromolar concentrations of adrenergic antagonists (which inhibited the prolongation of TTX block by epinephrine) did not prolong TTX block. Injection of adrenergic antagonists alone did not produce specific nerve block. They did not prolong TTX block when injected at a remote subcutaneous site. Prolongation of TTX block by phentolamine was not inhibited by co-injection with pertussis toxin. Adrenergic antagonists did not prolong bupivacaine block.

CONCLUSIONS

High concentrations of adrenergic antagonists markedly prolonged TTX block, but not bupivacaine block. This locally mediated action does not appear to be adrenergic-receptor-specific, or mediated by GTPase activation.

Functional analysis of patient-derived mutations in the Fanconi anemia gene, FANCG/XRCC9

OBJECTIVE

Fanconi anemia (FA) is an autosomal-recessive cancer susceptibility syndrome with seven complementation groups. Six of the FA genes have been cloned (corresponding to subtypes A, C, D2, E, F, and G) and the encoded proteins interact in a common pathway. Patient-derived mutations in FA genes have been helpful in delineating functional domains of FA proteins. The purpose of this work was to subtype FA patient-derived cell lines in our repository and to identify FA gene mutations.

METHODS

We subtyped 62 FA patients as type A, G, C, or non-ACG by using a combination of retroviral gene transfer and immunoblot analysis. Among these FA patients, we identified six FA-G patients for further analysis. We used a strategy involving amplification of FANCG/XRCC9 exons and direct sequencing to identify novel FANCG mutations in cell lines derived from these FA-G patients. We functionally analyzed FANCG mutant alleles by transducing the corresponding cDNAs into a known FA-G indicator cell line and scoring correction of MMC sensitivity.

RESULTS

Our results demonstrate a wide range of mutations in the FANCG gene (splice, nonsense, and missense mutations). Based on this mutational screen, a carboxy terminal functional domain of the FANCG protein appears to be required for complementation of FA-G cells and for normal assembly of the FANCA/FANCG/FANCC protein complex.

CONCLUSION

The identification of patient-derived mutant alleles of FA genes can provide important insights to the function of FA proteins. FA subtyping is also a necessary precondition for gene therapy.

[The diagnosis and treatment of quadrilateral space syndrome]

OBJECTIVE

To investigate the compression feature, clinical manifestation and the results of treatment of quadrilateral space syndrome.

METHODS

Four patients with axillary nerve entrapment at quadrilateral space had been treated and followed up for 5 to 12 months from May 1999 to June 2000. The causes, symptoms, signs and the treatment management of those cases were analyzed.

RESULTS

Among the 3 cases which received operation, sensation and motor function completely recovered in 2 cases and partially recovered in 1 case. No obvious recovery of sensation and motor function in the case which received local nerve blocking treatment.

CONCLUSION

The main diagnostic evidence for axillary nerve entrapment is the deltoid muscle paralysis and paresthesia in the lateral side of shoulder, and early neurolysis is recommended as soon as the diagnosis is clarified.

Global analysis of the Michaelis-Menten-type ratio-dependent predator-prey system

The recent broad interest on ratio-dependent based predator functional response calls for detailed qualitative study on ratio-dependent predator-prey differential systems. A first such attempt is documented in the recent work of Kuang and Beretta(1998), where Michaelis-Menten-type ratio-dependent model is studied systematically. Their paper, while contains many new and significant results, is far from complete in answering the many subtle mathematical questions on the global qualitative behavior of solutions of the model. Indeed, many of such important open questions are mentioned in the discussion section of their paper. Through a simple change of variable, we transform the Michaelis-Menten-type ratio-dependent model to a better studied Gause-type predator-prey system. As a result, we can obtain a complete classification of the asymptotic behavior of the solutions of the Michaelis-Menten-type ratio-dependent model. In some cases we can determine how the outcomes depend on the initial conditions. In particular, open questions on the global stability of all equilibria in various cases and the uniqueness of limit cycles are resolved. Biological implications of our results are also presented.