The stability of allyl radicals following the photodissociation of allyl iodide at 193 nm

The photodissociation of allyl iodide (C3H5I) at 193 nm was investigated by using a combination of vacuum-ultraviolet photoionization of the allyl radical, resonant multiphoton ionization of the iodine atoms, and velocity map imaging. The data provide insight into the primary C-I bond fission process and into the dissociative ionization of the allyl radical to produce C3H3+. The experimental results are consistent with the earlier results of Szpunar et al. [J. Chem. Phys. 119, 5078 (2003)], in that some allyl radicals with internal energies higher than the secondary dissociation barrier are found to be stable. This stability results from the partitioning of available energy between the rotational and vibrational degrees of freedom of the radical, the effects of a centrifugal barrier along the reaction coordinate, and the effects of the kinetic shift in the secondary dissociation of the allyl radical. The present results suggest that the primary dissociation of allyl iodide to allyl radicals plus I*(2P(1/2)) is more important than previously suspected.

Determination of spin-orbit branching fractions in the photodissociation of halogenated hydrocarbons

Two methods based on vacuum ultraviolet (vuv) photoionization are presented for the determination of the spin-orbit branching fractions of the halogen atom produced in the photodissociation of halogenated hydrocarbons. Both methods make use of differences in the photoionization cross sections of the 2P(3/2) ground state and the 2P(1/2) excited-state of the neutral halogen atom. In the first approach, measurements of the total photoionization signal of the halogen atom are made at several vuv wavelengths, and the difference in the wavelength dependences for the 2P(3/2) and 2P(1/2) atoms allows the extraction of the branching fractions. In the second approach, the vuv wavelength is set close to the ionization threshold of the 2P(3/2) atom (well above that of the 2P(1/2) atom), and measurements are made at several electric field strengths, which shift the ionization threshold and thus vary the photoionization cross sections. In both methods, the relative cross sections of the ground- and excited-state atoms are determined by using the known branching fractions for the 266 nm photodissociation of methyl iodide. These methods are applied to the photodissociation of isopropyl iodide and allyl iodide, two systems for which standard ion-imaging techniques do not provide unique branching fractions.

Immunogenicity of Empty Capsids of Porcine Circovius Type 2 Produced in Insect Cells

Porcine circovirus type 2 (PCV2), a single-stranded DNA virus, is associated with postweaning multisystemic wasting syndrome (PMWS). ORF2 protein (capsid) of PCV2 was recently demonstrated to be a major immunogenable to induce protection in pigs with a prime-boost protocol. In this study, the ORF2 gene of PCV2 was expressed in insect cells. The product self-assembled into particles that were structurally and antigenically indistinguishable from regular PCV2 capsids. To evaluated the immunogenicity of these virus-like particles, PCV2-free piglets were vaccinated with the crude lysate from recombinant baculovirus (Ac.ORF2)-infected insect cells, at doses of 0.1 ml (10(6) cells), 0.5 mL (5 x 10(6) cells) or 1.0 ml (10(7) cells). The immune response was monitored by an indirect enzyme-linked immunosorbent assay (ELISA) for PCV2 antibody and lymphocyte proliferation assay. The ELISA results indicated that primary immune response was elicited with 0.5 ml or 1.0 ml of crude lysate from Ac.ORF2. After boost immunization, relatively higher levels of PCV2 antibody were elicited in 0.5-ml or 1.0-ml vaccinated groups, compared to the 0.1-ml group. In addition, higher PCV2 specific lymphocyte proliferation response was developed in piglets vaccinated with 0.5 ml or 1.0 ml of crude lysate, especially in those vaccinated with with 1.0 ml of crude lysate. Thus, the expressed ORF2 protein has significant potential as a subunit vaccine against PCV2 infection.

LOI of IGF2 is associated with esophageal cancer and linked to methylation status of IGF2 DMR

In the present study, IGF2 mRNA expression was examined by semi-quantitative RT-PCR in 46 esophageal cancer cases. LOI of IGF2 was detected in informative samples, which were determined as heterozygote with ApaI polymorphism in exon 9 of IGF2 by PCR-RFLP and RT-PCR-RFLP. Methylation status of IGF2 DMR in informative samples was analyzed by sodium bisulfite treatment and PCR and the following cloning sequencing. The results showed that there was over-expression of IGF2 mRNA in tumor tissues (T) compared to their matched normal tissues (N) (P < 0.05). The expression level of IGF2 in tumor tissues was associated with pathological grades (P < 0.05), but proved irrelevant to clinical stages (P > 0.05). Of all informative samples, 21% (5/24) of cases showed there were IGF2 LOI; however, there was IGF2 LOI in the tumor tissue and not in its matched normal tissue in a special case. Methylation level of IGF2 DMR was average 29.7% in normal imprinting samples and 50.6% (P < 0.01) in IGF2 LOI separate samples. These data suggested that IGF2 may participate in carcinogenesis of esophageal cancer through its over-expression. IGF2 LOI may be one of the factors that lead to overexpression of IGF2 and may be at least partly due to aberrant methylation of IGF2 DMR in esophageal cancer.

Photodissociation of propargyl bromide and photoionization of the propargyl radical

Velocity map imaging was used to study the 193 nm photodissociation of propargyl bromide C(3)H(3)Br as well as the photoionization dynamics of the resulting propargyl radical C(3)H(3). Images were recorded by using single-photon vacuum ultraviolet ionization of the propargyl radical and by using two-photon resonant, three-photon ionization of the ground state Br((2)P(32)) and spin-orbit excited Br(*)((2)P(12)) atoms. Analysis of these data allowed the determination of the branching ratio Br:Br(*) as well as the photofragment angular distributions. Images of C(3)H(3) produced by the photodissociation of both C(3)H(3)Br and C(3)H(3)Cl were recorded at several energies between 8.97 and 9.12 eV, as well as at 9.86 eV, and showed no obvious internal energy dependence of the relative photoionization cross sections.

Near-threshold photoionization of hot isopropyl radicals

A combination of ion imaging and vacuum ultraviolet, single-photon ionization is used to study the internal energy dependence of the photoionization cross section of isopropyl radicals produced by the 266 nm photodissociation of isopropyl iodide. The isopropyl radicals so produced have internal energies of approximately 0.3-2.0 eV. Images recorded for photoionization energies from just below the adiabatic ionization threshold at 7.37+/-0.02 and 8.04 eV are essentially identical both to each other and to that recorded at 9.67 eV. These results imply that the photoionization cross section is only weakly dependent on internal energy. Several factors contributing to this observation are discussed, as are the implications for the photoionization of other systems with significant internal excitation.

Specific substitutions in the echinocandin target Fks1p account for reduced susceptibility of rare laboratory and clinical Candida sp. isolates

An association between reduced susceptibility to echinocandins and changes in the 1,3-beta-d-glucan synthase (GS) subunit Fks1p was investigated. Specific mutations in fks1 genes from Saccharomyces cerevisiae and Candida albicans mutants are described that are necessary and sufficient for reduced susceptibility to the echinocandin drug caspofungin. One group of amino acid changes in ScFks1p, ScFks2p, and CaFks1p defines a conserved region (Phe 641 to Asp 648 of CaFks1p) in the Fks1 family of proteins. The relationship between several of these fks1 mutations and the phenotype of reduced caspofungin susceptibility was confirmed using site-directed mutagenesis or integrative transformation. Glucan synthase activity from these mutants was less susceptible to caspofungin inhibition, and heterozygous and homozygous Cafks1 C. albicans mutants could be distinguished based on the shape of inhibition curves. The C. albicans mutants were less susceptible to caspofungin than wild-type strains in a murine model of disseminated candidiasis. Five Candida isolates with reduced susceptibility to caspofungin were recovered from three patients enrolled in a clinical trial. Four C. albicans strains showed amino acid changes at Ser 645 of CaFks1p, while a single Candida krusei isolate had a deduced R1361G substitution. The clinical C. albicans mutants were less susceptible to caspofungin in the disseminated candidiasis model, and GS inhibition profiles and DNA sequence analyses were consistent with a homozygous fks1 mutation. Our results indicate that substitutions in the Fks1p subunit of GS are sufficient to confer reduced susceptibility to echinocandins in S. cerevisiae and the pathogens C. albicans and C. krusei.

Immunocytochemical localization of gonadotropins during the development of XX and XY Nile tilapia

Gonadal development and steroidogenesis in teleosts is regulated by two gonadotropic hormones; luteinizing hormone (LH) and follicle-stimulating hormone (FSH). Earlier studies in tilapia have shown that FSH-beta and LH-beta appear by 14 days after hatching (dah), results from the current study corroborate with these previous reports in tilapia. Here we demonstrate the appearance of LH in pituitary between 14 and 20 dah. In addition to this the present study primarily focuses on any possible differences in appearance of LH-beta and FSH-beta immunoreactivity between XX and XY population of Nile tilapia. LH immunoreactivity was found to be lower in pituitary of XX fish when compared to XY fish. The development of FSH-beta immunoreactivity in pituitary of the Nile tilapia is also presented. Overall, it remains to be established what significance these findings on the appearance of gonadotropins hold for sex differentiation in tilapia.

X-ray microtomographic study of mineral concentration distribution in deciduous enamel

OBJECTIVE

To determine the mineral concentration distribution in deciduous enamel by quantitative X-ray microtomography (XMT).

DESIGN

Tooth rods ( approximately 2 mm x 2 mm) were removed from the mid-buccal region of 11 deciduous molars. Three XMT slices were taken at 1.5, 2.0 and 2.5 mm from the amelocemental junction. The distribution and variation in mineral concentration of enamel were studied from the XMT images.

RESULTS

The mean mineral concentration for all the teeth was 2.81 (S.D. = 0.065) g cm(-3). There was no notable difference in the mean mineral concentration values between the three XMT slices of each tooth. However, there was up to 8% variation between different teeth (2.69-2.92 g cm(-3)). Gradients of increasing mineral concentration from the amelodentinal junction (ADJ) to the external surface were found, ranging from 0.08 to 0.60 mg cm(-3) microm(-1) with a mean of 0.366 mg cm(-3) microm(-1). The mineral concentration gradients in the occlusal slices were steeper than those in the cervical slices. The difference in mineral concentration between the inner and outer enamel ranged from 1.5 to 8.7%.

CONCLUSION

In view of the large variation in both the means and the gradients of mineral concentration in deciduous molars, the mineral distribution of each experimental tooth should be measured as baseline data in studies of caries progression.

A new iterative procedure for combining direct methods with solvent flattening - dealing with the phase ambiguity in protein crystallography

A new procedure for combining direct methods with the solvent-flattening technique is proposed for phasing single isomorphous replacement (SIR) or one-wavelength anomalous scattering (OAS) data of proteins. The new procedure differs from the previous one [Zheng, Zheng, Gu, Mo, Fan & Hao (1997). Acta Cryst. D53, 49-55] in that the direct method not only provides input phases to but also accepts feedback phases from solvent flattening, thus forming an iterative process for breaking the ambiguities and refining the values of phases. The new procedure was tested with the experimental SIR data of the known structure ribonuclease Sa. For the strongest 1000 of the total 7264 reflections, the mean F(obs)-weighted phase error is 7.5 and 9.4 degrees lower than that of the previous procedure and that of solvent flattening alone, respectively.

Atomic force microscopy investigation of isolated virions of murine leukemia virus

Virions of mouse leukemia virus spread on glass substrates were visualized by atomic force microscopy. The size distribution mode was 145 nm, significantly larger than that for human immunodeficiency virus particles. The distribution of particle sizes is broad, indicating that no two particles are likely identical in content or surface features. Virions possess knoblike protrusions, which may represent vestiges of budding from cell membranes. Particles which split open allowed imaging of intact cores with diameters of 65 nm. They also permitted estimation of viral shell thickness (35 to 40 nm) and showed the presence of a distinct trough between the shell and the core surface.

Selective recovery of striatal 125I-alpha-conotoxinmii nicotinic receptors after nigrostriatal damage in monkeys

Evidence suggests that nicotinic receptors play a role in nigrostriatal function, a finding that may be relevant to Parkinson's disease. Knowledge of the conditions that regulate nicotinic receptor expression is therefore important. Previous studies showed that several different nicotinic receptors, including alpha-conotoxinMII (alpha-CtxMII)-sensitive receptors, are decreased after nigrostriatal damage. Nigrostriatal dopaminergic terminals also demonstrate a capacity for recovery after lesioning. The present experiments were therefore done to determine whether there were changes in striatal nicotinic receptors with recovery. To address this, we used two well-characterized animal models of nigrostriatal damage produced using the selective dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Studies in mice showed that striatal 125I-alpha-CtxMII, as well as 125I-epibatidine and 125I-A85380 binding sites significantly recovered 1 month after lesioning, suggesting that alpha6* and most likely alpha4* receptors are increased. Experiments were next done in monkeys since striatal 125I-alpha-CtxMII receptors constitute a large percentage of nicotinic receptors and are more vulnerable to nigrostriatal damage in this model that closely mirrors Parkinson's disease. In monkeys allowed to recover from the toxic effects of MPTP for a 1-2 year period, there was a significant improvement in the Parkinson disability score. There was also a reversal in lesion-induced declines in striatal alpha-CtxMII-sensitive receptors, but no significant change in 125I-epibatidine and 125I-A85380 receptors. These findings suggest that alpha3*/alpha6* sites are selectively increased in monkey striatum with recovery. The present data show that recovery of 125I-alpha-CtxMII receptors occurs in parallel with the dopamine transporter, indicating that these nicotinic receptors sites are localized to presynaptic dopamine terminals in both species.

Atomic force microscopy imaging of retroviruses: human immunodeficiency virus and murine leukemia virus

Retroviruses are membrane-enveloped, RNA-containing viruses that produce a wide range of threatening diseases in higher animals. Among these are human immunodeficiency virus (HIV), which produces acquired immune deficiency syndrome (AIDS) in humans, and murine leukemia virus (MuLV), which produces leukemias in rodents. We have obtained the first atomic force microscopy (AFM) images of these two retroviruses, both isolated from culture media and emerging from infected cell surfaces. The HIV virions are 127 nm diameter on average, and those of MuLV are 145 nm, although there are wide distributions about the means. The AFM images show the arrangement of the envelope protein, responsible for host cell entry, on the surfaces of both virions. Disruption of the viruses using detergents or physical means allowed us to visualize interior structures, including the outer shells of both MuLV and HIV, the cores of MuLV, and the nucleic acid of HIV complexed with core proteins. Using immunolabeling techniques borrowed from electron microscopy, we were able to demonstrate the binding of gold-labeled antibodies directed against the envelope protein of MuLV. The AFM images are revealing, not only in terms of surface topology, but in terms of interior features as well, and they reveal the eccentricities and uniqueness of individual virus particles rather than yielding the average member of the population. Further application of AFM to viruses associated with other pathologies may ultimately have a significant impact on the diagnosis and treatment of virus-promoted diseases.

Atomic force microscopy investigation of wild-type Moloney murine leukemia virus particles and virus particles lacking the envelope protein

Moloney murine leukemia virus (M-MuLV) lacking the gene for the envelope glycoprotein (env(-)) was produced in NIH 3T3 cells and investigated using atomic force microscopy (AFM). The particles were compared with similarly produced wild-type virions, some of which had been exposed to a monoclonal antibody against the surface component of the envelope protein (SU protein). The env(-) particles generally exhibit a distinctly different external appearance suggesting only a low density of associated proteins that have an almost fluid, mechanically unstable character. The weakly associated proteins may be host cell membrane proteins that are incorporated into the viral membrane in place of or in addition to virus envelope protein. The amount of this non-viral protein on virion surfaces appears to vary from negligible in most cases to a substantial complement in others. It seems clear that the presence of the envelope protein, in a mechanical sense, significantly strengthens and stabilizes the virion envelope. Binding of monoclonal antibody to wild-type virions indicates that some particles expose a significant amount of antigen while adjacent virions may not. This suggests that the conformation of the envelope glycoprotein or the disposition of oligosaccharides may be different among particles, on some virions exposing the specific epitope, and others little or none.

[Dynamic changes in amino acid and glucose in culture medium with adult Schistosoma japonicum]

OBJECTIVE

To observe the dynamic changes in the contents of amino acid(AA), glucose(Gluc) and triglyceride(TG) in the culture medium containing adult Schistosoma japonicum.

METHODS

The contents of AA, Gluc and TG in the culture medium during the incubation period for d0 to 6 d were detected by amino acid automatic analyzer and automatic biochemical analyzer.

RESULTS

The contents of Arg, Thr, Met, and Lys and Gluc were reduced, Asp and Ala increased apparently. CONCLUASION: Increasing the levels of Arg, Thr, Met Lys and Gluc, reducing the levels of Asp and Ala, and changing the culture medium in time might be in favor of the in vitro cultivation of S. japonicum.

Molecular biology of jaagsiekte sheep retrovirus

Jaagsiekte sheep retrovirus (JSRV) is the causative agent of ovine pulmonary adenocarcinoma (OPA), a contagious lung cancer of sheep. Until recently, research on JSRV/OPA was hampered by the lack of a tissue culture system for the propagation of the virus. Historically, pathological samples (lung fluid) collected from sheep affected by OPA were the only source of infectious JSRV. Thus studies on the JSRV/OPA system were conducted only where field isolates of OPA cases were readily available. In the past 10 years, the deduction of the JSRV sequence (York et al. 1991; York 1992), the isolation of an infectious and oncogenic JSRV molecular clone (JSRV21) (Palmarini et al. 1999a) and the establishment of a rapid method to produce infectious virus in vitro (Palmarini et al. 1999a) sparked many studies at the molecular level that strengthened past observations and revealed new properties of this unique virus. Here, we will review the data accumulated so far on the molecular biology of JSRV using the infectious and oncogenic JSRV21 molecular clone as virus of reference.

Transformation and oncogenesis by jaagsiekte sheep retrovirus

Jaagsiekte sheep retrovirus (JSRV) is an exogenous retrovirus of sheep that induces a contagious lung cancer, ovine pulmonary adenocarcinoma (OPA). JSRV is a potent carcinogen in the experimental setting, inducing end-stage tumors at around 6 weeks of age when newborn lambs are inoculated intratracheally. Despite this rapid oncogenesis, inspection of the JSRV genome sequence does not reveal any obvious viral oncogenes. In this review, recent advances in studies of JSRV oncogenic transformation are described. Molecular cloning of an infectious and oncogenic JSRV provirus was instrumental in the studies. DNA transfection of JSRV proviral DNA into mouse NIH3T3 cells results in morphological transformation, indicating that the JSRV genome carries an oncogene. Further experiments identified the JSRV envelope protein as the transforming gene, and a PI3 kinase docking site in the cytoplasmic tail of the transmembrane (TM) protein was shown to be necessary for transformation. Avian DF-1 cells infected with an avian retroviral vector (RCAS) expressing the JSRV envelope protein also undergo tumorigenic transformation. Possible mechanisms of transformation are discussed, and a cooperating role for insertional activation of proto-oncogenes in tumorigenesis is also considered. The transforming potential of the JSRV envelope protein may be necessary for JSRV infection and replication in vivo.

The Effects of Reservoir Minerals on the Composition Changes of Heavy Oil During Steam Stimulation

Abstract

The catalytic effect of minerals on the hydrocarbon groups, viscosity, and element distribution of heavy oil during the thermal recovery process studied are in this paper. The results show that minerals have a catalytic effect in the aquathermolysis of heavy oil. When 10 wt% mineral was added to the reaction system, the saturate and aromatic content increased, while the resins and asphaltenes components decreased. The results also show that the average molecular weight of heavy oil and asphaltene was reduced after treatment, and the content of sulphur decreased. The viscosity of the heavy oil used in our study decreased by 23.4 - 25.6% in the reaction system after treatment with steam.

Introduction

Thermal recovery processes have been the most effective EOR technologies to recover heavy oil in the world. In addition to the fact that steam can reduce the viscosity of heavy oil, there are chemical reactions between steam and heavy oil. It has been observed that this chemical reaction can play an important role in the process and induce the formation of gaseous components such as carbon dioxide, hydrogen sulfide, and hydrogen during steam injection. Hyne et al. used the term "aquathermolysis" to describe the chemical interaction of high-temperature, high-pressure water with the reactive components of heavy oil and tar sands bitumen, and to distinguish this process from the term "hydrothermolysis" which has come to be associated with the interaction with hydrogen at elevated temperature and pressure(1). Their results, obtained from model compounds, show that some mineral components, in particular trace metals such as vanadium and nickel, can accelerate the breakdown of organosulphur components present in heavy oil, producing carbon monoxide and other gases noted previously. The aquathermolysis of heavy oil can result in an increase in the content of saturates and aromatics and a decrease in resins and asphaltenes, lowering the average molecular weight and viscosity, and improving the properties of the oil.

Many researchers have studied how to apply reservoir minerals to accelerate the aquathermolysis of heavy oil to realize down-hole catalytic upgrading of heavy oil. Belgrave et al. investigated the kinetic models for the aquathermolysis of heavy oil and pointed out that the mineralogy plays an important role in the generation of CO2 and H2S(2). Clark et al. studied the steam-oil chemical reaction and pointed out that some of metal ions, minerals, and reservoir sands can result in the change of composition of heavy oil(3, 4). Monin et al. have studied the thermal cracking of heavy-oil/mineral matrix systems at temperature and pressures encountered during thermal recovery. They pointed out that chemical reactions involving oil, possibly water, and mineral matrix may lead to significant changes in composition of the heavy oil. Their work focused on four thermal crude oils with different geochemical compositions. They observed that a large number of light hydrocarbons, CO2, and H2S was produced if minerals existed in the reaction system(5) Hamid Pahlavan et al. also studied the geochemical changes of heavy crude oil during thermal recovery(6).

Involvement of semicarbazide-sensitive amine oxidase-mediated deamination in atherogenesis in KKAy diabetic mice fed with high cholesterol diet

AIMS/HYPOTHESIS

Semicarbazide-sensitive amine oxidase has been recognised to be a potential risk factor in vascular disorders associated with diabetic complications and to be related to mortality in patients suffering from heart disease. This enzyme, associated with the vascular system, catalyses the deamination of methylamine and aminoacetone, and also acts as an adhesion molecule related to leucocyte trafficking and inflammation. The deaminated products include the toxic aldehydes, formaldehyde and methylglyoxal, respectively, hydrogen peroxide and ammonia.

MATERIALS AND METHODS

In this study, the KKAy mouse, a strain possessing features closely resembling those of Type II (non-insulin-dependent) diabetes mellitus has been used to substantiate the hypothesis. Vascular lesions were induced via chronic feeding of a high cholesterol diet.

RESULTS

Both MDL-72974A, a selective mechanism-based semicarbazide-sensitive amine oxidase inhibitor and aminoguanidine effectively inhibited aorta semicarbazide-sensitive amine oxidase activity, and caused a substantial increase in urinary methylamine, and a decrease in formaldehyde and methylgloxal levels. Inhibition of semicarbazide-sensitive amine oxidase also reduced oxidative stress, as shown by a reduction of malondialdehyde excretion. Both MDL-72974A and aminoguanidine reduced albuminuria, proteinuria and the number of atherosclerotic lesions in animals fed with a cholesterol diet over a period of treatment for 16 weeks.

CONCLUSION/INTERPRETATION

Increased semicarbazide-sensitive amine oxidase-mediated deamination could be involved in the cascade of atherogenesis related to diabetic complications.

Epstein-Barr viral load measurement as a marker of EBV-related disease

Epstein-Barr virus (EBV) is associated with a wide variety of benign and neoplastic diseases. EBV viral load assays that may prove useful in rapid assessment of disease status are now available. The two most common approaches to viral load measurement are quantitative, competitive PCR, and real-time PCR. Laboratory studies have shown that these assays are sensitive and specific for measuring EBV DNA in blood samples. Clinical investigations suggest a role for viral load measurement in predicting and monitoring EBV-associated tumors, including nasopharyngeal carcinoma, post-transplant lymphoproliferative disorder, Hodgkin's disease, and AIDS-related lymphoma. These new laboratory tools show promise in improving clinical management of affected patients.

A tobacco nuclear extract supporting transcription, processing, splicing and modification of plant intron-containing tRNA precursors

Nuclear tRNA genes are transcribed by RNA polymerase III (Pol III) and pre-tRNAs are processed into mature tRNAs via complex processes in the nucleus. We have developed an in vitro Pol III-dependent transcription system derived from tobacco cultured cells, which supports efficiently not only transcription of a variety of plant tRNA genes but also 5'-and 3'-end processing, nucleotide modification and splicing of intron-containing pre-tRNAs. The structures of in vitro transcripts have been confirmed by primer extension analysis and by RNase T1 fingerprinting. The optimal Mg2+ concentration differed for each step so that each reaction can be controlled by adjusting the Mg2+ concentration. At 1 mm Mg2+, only transcription occurs so that pre-tRNAs accumulate. The splicing reaction can be initiated by raising Mg2+ ions (> 5 mm) and enhanced by adding 1 mm hexamminecobalt chloride. Using the optimized system for the Nicotiana intron-containing tRNATyr gene, the precise initiation and termination sites of transcription and the splice sites were determined. The presence of 1 mm NAD+ in the reaction mixture leads to the removal of the 2' phosphate at the splice junction of tRNATyr, demonstrating the activity of a 2'-phosphotransferase in the tobacco nuclear extract. Many modified nucleosides such as m2G, m22G, m1A, phi27 and phi35 are introduced in either of the studied transcripts. As shown in other systems, the conversion of U35 to phi requires an intron-containing substrate.

Expression of endogenous betaretroviruses in the ovine uterus: effects of neonatal age, estrous cycle, pregnancy, and progesterone

The ovine genome contains 15 to 20 copies of endogenous retroviruses (enJSRVs) highly related to the oncogenic jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus. enJSRVs are highly expressed in the endometrial lumenal epithelia (LE) and glandular epithelia (GE) of the ovine uterus. The effects of neonatal age, estrous cycle, pregnancy, and progesterone on expression of enJSRVs in the ovine uterus were determined. Expression of enJSRV RNAs was absent from the uterus of ewes at birth, but enJSRV RNAs were expressed specifically in the LE and developing GE from postnatal day (PND) 7 to PND 56. In adult ewes, enJSRV RNAs were detected only in the epithelia of the uterine endometrium, as well as epithelia of the oviduct, cervix, and vagina. In cyclic ewes, endometrial enJSRV RNA abundance was lowest on day 1, increased 12-fold between days 1 and 13, and then decreased to day 15. In pregnant ewes, levels of endometrial enJSRV RNAs were high on day 11, increased to day 13, and then decreased to day 19. In day 17 and 19 conceptuses, enJSRV RNAs were also detected in binucleate cells of the trophectoderm. Immunoreactive JSRV capsid and envelope proteins were detected in the endometrial LE and GE, as well as in the binucleate cells of the conceptus. In transfection assays utilizing ovine endometrial LE cells, progesterone increased transcriptional activity of several enJSRV long terminal repeats. Collectively, these results indicate that transcription of enJSRVs in the endometrial epithelia of the ovine uterus is increased by progesterone and might support a role for enJSRVs in conceptus-endometrium interactions during the peri-implantation period and early placental morphogenesis.

Analytic validation of a competitive polymerase chain reaction assay for measuring Epstein-Barr viral load

Epstein-Barr virus (EBV) is associated with several benign and malignant diseases, and blood tests for EBV viral load show promise as markers of disease burden in affected patients. A commercial quantitative PCR method (BioSource International) was recently introduced to facilitate measuring viral load. It relies on coamplification of EBV DNA and a spiked competitor in plasma or serum, followed by semiautomated product detection on enzyme-linked immunosorbent assay (ELISA) plates. In the current study, analytic performance characteristics were assessed, and the authors describe several methodologic improvements to facilitate laboratory implementation. Rapid DNA extraction was accomplished using commercial silica spin columns, heat-labile uracil-N-glycosylase was used to inhibit amplicon contamination, and inexpensive agarose gels were used to screen for polymerase chain reaction products requiring ELISA plate quantitation. Accuracy and precision were verified using EBV DNA standards derived from two cell lines and plasmid containing viral sequences. The assay was sensitive to as few as five template copies per polymerase chain reaction and was linear across four orders of magnitude (correlation coefficient 0.995). When applied to matched plasma and serum samples from 15 patients with nasopharyngeal carcinoma, both sample types yielded similar viral load results. This commercial EBV viral load assay provides sensitive and quantitative detection of EBV DNA using equipment already available in many molecular diagnostic laboratories.

Retrovirus-induced ovine pulmonary adenocarcinoma, an animal model for lung cancer

Studies on the molecular mechanisms of transformation of retrovirus-induced neoplasms in domestic and laboratory animal species have provided insights into the genetic basis of cancer. Ovine pulmonary adenocarcinoma (OPA) is a retrovirus-induced spontaneous lung tumor of sheep that has striking analogies to some forms of human adenocarcinoma. The etiologic agent of OPA, jaagsiekte sheep retrovirus (JSRV), is unique among retroviruses for having a specific tropism for the differentiated epithelial cells of the lung, and it is the only virus known to cause a naturally occurring lung adenocarcinoma. Expression of the JSRV envelope protein is sufficient to induce cell transformation in vitro, possibly via the activation of the phosphatidylinositol 3-kinase/Akt-signaling pathway mediated by the cytoplasmic tail of the transmembrane protein. The aim of this review is to draw the attention of basic and clinical scientists engaged in lung cancer research to this unique animal model, to explore the possible use of OPA as a tool to investigate the mechanisms of pulmonary carcinogenesis, and to underline the similarities between OPA and some forms of human lung adenocarcinoma. The possibility of a viral etiology for the latter will be evaluated in this review.

[125/123I] 5-Iodo-3-pyridyl ethers. syntheses and binding to neuronal nicotinic acetylcholine receptors

Three 3-pyridyl ether nicotinic ligands-(S)-5-Iodo-3-[(2-pyrrolidinyl)-methoxy]pyridine (5-iodo-A-85865), (S)-5-Iodo-3-[1-(methyl)-2-pyrrolidinyl-methoxy]pyridine (5-Iodo-A-84543), and (S)-5-iodo-3-[1-methyl-(2-azetidinyl)-methoxy]pyridine (5-iodo-N-Me-A-85380) were labeled with I-125/I-123, and their ability to label high-affinity brain nicotinic acetylcholine receptors (nAChRs) was evaluated. The most promising ligand, [123/125I] 5-iodo-A-85865, showed approximately 65% inhibition of radioactivity uptake in thalamus in mice pretreated with cytisine. Preliminary SPECT imaging studies with [123I] 5-iodo-A-85865 revealed a distribution profile consistent with nAChRs (thalamus > frontal cortex > cerebellum) and a more rapid pharmacokinetic profile relative to azetidinyl 3-pyridyl ether based ligands.

Structure-based ligand design for flexible proteins: application of new F-DycoBlock

A method of structure-based ligand design - DycoBlock - has been proposed and tested by Liu et al. It was further improved by Zhu et al. and applied to design new selective inhibitors of cyclooxygenase 2. In the current work, we present a new methodology - F-DycoBlock that allows for the incorporation of receptor flexibility. During the designing procedure, both the receptor and molecular building blocks are subjected to the multiple-copy stochastic molecular dynamics (MCSMD) simulation, while the protein moves in the mean field of all copies. It is tested for two enzymes studied previously - cyclooxygenase 2 (COX-2) and human immunodeficiency type 1 (HIV-1) protease. To identify the applicability of F-DycoBlock, the binding protein structure was used as starting point to explore the conformational space around the bound state. This method can be easily extended to accommodate the flexibility in different degree. Four types of treatment of the receptor flexibility - all-atom restrained, backbone restrained, intramolecular hydrogen-bond restrained and active-site flexible - were tested with or without the grid approximation. Two inhibitors, SC-558 for COX-2 and L700417 for HIV-1 protease, are used in this testing study for comparison with previous results. The accuracy of recovery, binding energy, solvent accessible surface area (SASA) and positional root-mean-square (RMS) deviation are used as criteria. The results indicate that F-DycoBlock is a robust methodology for flexible drug design. It is particularly notable that the protein flexibility has been perfectly associated with each stage of drug design - search for the binding sites, dynamic assembly and optimization of candidate compounds. When all protein atoms were restrained, F-DycoBlock yielded higher accuracy of recovery than DycoBlock (100%). If backbone atoms were restrained, the same ratio of accuracy was achieved. Moreover, with the intramolecular hydrogen bonds restrained, reasonable conformational changes were observed for HIV- 1 protease during the long-time MCSMD simulation and L700417 was reassembled at the active site. It makes it possible to study the receptor motion in the binding process.

A phosphatidylinositol 3-kinase docking site in the cytoplasmic tail of the Jaagsiekte sheep retrovirus transmembrane protein is essential for envelope-induced transformation of NIH 3T3 cells

Jaagsiekte sheep retrovirus (JSRV) is the causative agent of a transmissible lung cancer of sheep known as ovine pulmonary carcinoma. Recently, we have found that the expression of the JSRV envelope (Env) is sufficient to transform mouse NIH 3T3 cells in classical transformation assays. To further investigate the mechanisms of JSRV oncogenesis, we generated a series of envelope chimeras between JSRV and the JSRV-related endogenous retroviruses of sheep (enJSRVs) and assessed them in transformation assays. Chimeras containing the exogenous JSRV SU region and the enJSRV TM region were unable to transform NIH 3T3 cells. Additional chimeras containing only the carboxy-terminal portion of TM (a region that we previously identified as VR3) of the endogenous envelope with SU and the remaining portion of TM from the exogenous JSRV were also unable to transform NIH 3T3 cells. The VR3 region includes the putative membrane-spanning region and cytoplasmic tail of the JSRV TM glycoprotein; this suggested that the cytoplasmic tail of the JSRV Env mediates transformation, possibly via a cell signaling mechanism. Mutations Y590 and M593 in the cytoplasmic tail of the JSRV envelope were sufficient to inhibit the transforming abilities of these constructs. Y590 and M593 are part of a Y-X-X-M motif that is recognized by the phosphatidylinositol 3-kinase (PI-3K). PI-3K initiates a cell signaling pathway that inhibits apoptosis and is required for a number of mitogens during the G(1)-to-S-phase transition of the cell cycle. PI-3K activates Akt by phosphorylation of threonine 308 and serine 473. We detected by Western blot analysis phosphorylated Akt in serum-starved MP1 cells (NIH 3T3 cells transformed by JSRV) but not in the parental NIH 3T3 cells. These data indicate that the cytoplasmic tail of the JSRV TM is necessary for cell transformation and suggest a new mechanism of retroviral transformation. In addition, the ability to dissociate the function of the JSRV envelope to mediate viral entry from its transforming capacity has direct relevance for the design of JSRV-based vectors that target the differentiated epithelial cells of the lungs.

[Thymoma-report of 166 patients]

OBJECTIVE

To discuss the characteristics of operation and the prognosis of 166 patients with thymoma.

METHODS

166 thymoma patients were treated from February 1985 to February 2000. By Masaoka staging system, there were 102 (61.4%) stage I, 28 (16.9%) stage II, 24 (14.5%) stage III, 12 (7.2%) stage IV a and 0 stage IV b lesions. The relation between stage and survival rate was analyzed.

RESULTS

One (0.6%) patient died of the operation. 137 (82.5%) patients underwent radical operation. Thirty patients were lost to follow-up. With the life table method, the 10-year survival rate was 56.8%, with 79.8% for stage I, 51.6% for stage II, 33.5% for stage III and 0% for stage IV patients.

CONCLUSION

Diagnosis of thymoma still depends on both clinical and pathological findings, which are correlated with stage. The principal treatment is to resect the tumor as completely as possible so as to relieve the symptoms and prolong the life of the patient.

Cytochrome oxidase activity is increased in +/Lc Purkinje cells destined to die

+/Lc Purkinje cells degenerate postnatally because of a gain-of-function mutation in the delta2 glutamate receptor (Grid2) that causes a constitutive Na+ current leak. The effect of the resulting chronic depolarization on Purkinje cell metabolism was investigated by measuring levels of cytochrome oxidase (COX) activity in Purkinje cell dendrites using quantitative densitometry. Analysis of wild type controls and +/Lc mutants at P10, P15 and P25 showed that levels of COX activity were significantly increased above control levels by P15 and continued to increase through P25. The increase in COX activity is likely to reflect an increase in oxidative phosphorylation to accommodate the energy demands of removing excess Na+ and Ca2+ entering the Purkinje cells in response to the Grid2 leak current.

Do ethanol and deuterium oxide distribute into the same water space in healthy volunteers?

BACKGROUND

The volume of distribution at steady state for ethanol (Vss) is thought to be identical to the total body water (TBW). We compared a two-compartment pharmacokinetic model with parallel Michaelis-Menten and first-order renal elimination with the classical one-compartment zero-order elimination model. Ethanol concentration-time profiles were established for breath, venous blood, and urine. The values of Vss obtained for ethanol were compared with TBW determined by deuterium oxide dilution.

METHODS

Sixteen healthy volunteers each received a 30-min intravenous infusion of ethanol on two occasions. Ethanol was measured in breath by a quantitative infrared analyzer and in blood and urine by headspace gas chromatography. Deuterium oxide was given as an intravenous injection and measured in serum by isotope-ratio mass spectrometry. Components of variation were calculated by ANOVA to determine the precision of the estimates of Vss and TBW.

RESULTS

Mean TBW, determined by deuterium oxide dilution, was 44.1 +/- 3.9 liters (+/-SD) for men, corresponding to 0.61 liters/kg, and 37.4 +/- 3.2 liters for women, or 0.54 liters/kg. Estimates of Vss from blood-ethanol pharmacokinetics were 87.6% of TBW according to isotope dilution and 84.4% for breath analysis with the two-compartment model. This compares with 95.1% and 95.4% for blood and breath alcohol, respectively, when the classical zero-order kinetic analysis is used. The precision of the estimates of Vss and TBW was between +/-1.56 and +/-2.19 liters (95% confidence interval).

CONCLUSIONS

Ethanol does not distribute uniformly into the TBW. The precision of measuring Vss by ethanol dilution was comparable to estimates of TBW by isotope dilution. Results of noninvasive breath ethanol analysis compared well with use of venous blood for estimating Vss. The sophisticated two-compartment model was much superior to the classical one-compartment model in explaining the total concentration-time course of intravenously given ethanol.

Sustainable systemic delivery via a single injection of lentivirus into human skin tissue

The skin offers a tissue site accessible for delivery of gene-based therapeutics. To develop the capability for sustained systemic polypeptide delivery via cutaneous gene transfer, we generated and injected pseudotyped HIV-1 lentiviral vectors intradermally at a range of doses into human skin grafted on immune-deficient mice. Unlike Moloney murine leukemia virus (MLV)-based retrovectors, which failed to achieve detectable cutaneous gene transfer by this approach, lentivectors effectively targeted all major cell types within human skin tissue, including fibroblasts, endothelial cells, keratinocytes, and macrophages. After a single injection, lentivectors encoding human erythropoietin (EPO) produced dose-dependent increases in serum human EPO levels and hematocrit that increased rapidly within one month and remained stable subsequently. Delivered gene expression was confined locally at the injection site. Excision of engineered skin led to rapid and complete loss of human EPO in the bloodstream, confirming that systemic EPO delivery was entirely due to lentiviral targeting of cells within skin rather than via spread of the injected vector to visceral tissues. These findings indicate that the skin can sustain dosed systemic delivery of therapeutic polypeptides via direct lentivector injection and thus provide an accessible and reversible approach for gene-based delivery to the bloodstream.

The membrane-bound but not the soluble form of human Fas ligand is responsible for its inflammatory activity

The ectopic expression of Fas ligand (FasL/CD95L) in tissues or tumors induces neutrophil infiltration and the destruction of the tissues or the rejection of tumors. It has been suggested that the infiltrated neutrophils are responsible for the latter phenomena. FasL is synthesized as a type II transmembrane protein, and soluble FasL is produced by a proteolytic mechanism from the membrane-bound form. We previously demonstrated that uncleavable membrane-bound FasL of mice induces IL-1 beta release from inflammatory cells, and suggested that the IL-1 beta enhances neutrophil infiltration. However, recent papers reported that human soluble FasL is directly chemoattractive to neutrophils in vitro and proposed that the soluble form of FasL is responsible for its inflammatory activity. Therefore, in this report, we investigated which form is responsible for the inflammatory activities of human FasL. We produced tumor cell lines expressing one or both forms of human FasL. Cells expressing both forms or only the membrane-bound form of FasL induced neutrophil infiltration when transplanted into the peritoneal cavity of syngeneic mice, while cells expressing only the soluble form did not. Purified soluble FasL failed to induce neutrophil infiltration in vivo. IL-1 beta release from inflammatory peritoneal exudate and acceleration of tumor rejection were also mediated by membrane-bound but not soluble FasL. These results indicate that the membrane-bound form of FasL is primarily responsible for its inflammatory activity.

Elimination of Bax expression in mice increases cerebellar purkinje cell numbers but not the number of granule cells

Cerebellar Purkinje cells and granule cells have been studied extensively as models for investigating neuron-target interactions and the regulation of cell numbers in the developing central nervous system. Recent studies of transgenic mice that overexpress a human Bcl-2 transgene in Purkinje cells suggest both that programmed cell death plays an unexpected role in regulating Purkinje cell number and that Purkinje cells influence the number of granule cells. The role of cell death-related proteins and Purkinje-granule cell interactions in cerebellar development was investigated further in this study by counting the number of Purkinje and granule cells in knockout mutants with a deletion in the proapoptotic gene, Bax. The total number of Purkinje cells was estimated using stereological counting principles in six adult wild type mice, four hemizygous Bax +/- controls, and six Bax -/- knockout mutants. The total number of granule cells per cerebellum was estimated in three adult wild type mice, three hemizygous Bax +/- controls, and three Bax -/- knockout mutants. The number of Purkinje cells increased significantly by over 30% in the Bax -/- knockout mutants compared with wild type and hemizygote controls, whereas the number of granule cells was unchanged in the Bax -/- mutants. There was no change in the volume of the cerebellar cortex or in the size of Purkinje cell bodies in the Bax -/- mutants, implying that Purkinje cell density was increased in the Bax -/- mutants. The increase in Purkinje cell numbers in the Bax -/- knockout mice supports previous evidence that Purkinje cells undergo a period of naturally occurring cell death that is mediated at least in part by the cell death proteins Bcl-2 and Bax. The lack of an effect of Bax gene expression on granule cell numbers indicates that Bax is not an obligate participant in naturally occurring cell death in granule cells.

Vanadium, molybdenum, and sodium triethanolamine complexes derived from an assembly system containing tetrathiometalate and triethanolamine

The reaction system composed of triethanolamine (TEA) and tetrathiovanadate in the presence of MeONa (MeOLi) or NaNH2 was studied to afford vanadium and alkali metal TEA complexes. Complexes [M subsetV6O6[N(CH2CH2O)2(CH2CH2OH)]6]2S6 (M = Na (1), Li (2)) contain two cyclic V((IV)) [12]metallacrown-6 cations linked by a polysulfide S6(2-) anion. Also separated from the reaction system is a novel sodium TEA complex [[Na(TEA)]2S6]n (3), in which parallel coordination chains [Na(TEA)+]n are connected by O-H...S hydrogen bonds forming 3-D network structure. Variable-temperature conductance of 3 was determined to display semiconductor feature. The desulfurization of VS4(3-) was observed to form S6(2-) anion and/or S8 molecule in the synthetic reactions of 1-3. A striking contrast was noted that MoS4(2-) did not desulfurize in the similar reaction to that of VS4(3-) with TEA, and a Na/TEA complex containing MoS4(2-), (Et4N)2[Na2(mu-TEA)2(CH3OH)2](MoS4)2 (4), was obtained instead. The S...H-O and O...H-O hydrogen bonds play an important role in forming the one- or three-dimensional structures for all these complexes by the linkages between clusters and chains. The IR spectrum indicates the structural similarity of complexes 1 and 2. For complex 4, the Mo=S stretch vibration at 468 cm(-1) showing widening and slight red-shift and the slight movement of the 1H NMR signals of TEA ligand to downfield are considered to be the influence of the S...H-O hydrogen bonds. Variable temperature magnetic susceptibility data were collected for complex 1. The effect magnetic moment per V6 unit varies gradually from 4.04 muB at 300 K to 6.24 muB at 5 K, exhibiting ferromagnetic interaction. Heisenberg-type vector-coupling model and molecular field approximation were used to treat the interaction between the paramagnetic sites and gave a good fitting result: J = 3.97 cm(-1), J' = 1.99 cm(-1), g = 1.99, F = 3.64 x 10(-3). Density functional calculation was also performed to complex 1 and its Li, K analogues. The lowest total bonding energy of -874.001 eV was obtained for [Na subsetV6(mu3-O)6] complex containing six unpaired electrons, indicating the stability of a V6 system with six independent spins S = 1/2. When the alkali metal ion is inserted into the [V6(mu3-O)6] cavity, the positive values of the bonding interaction (E(b)) indicate that the insertion depresses the total energy and that complexes 1 and 2 together with K+ complex may exist. However, the lowest E(b) value of the K+ complex implies its instability.

The helper virus envelope glycoprotein affects the disease specificity of a recombinant murine leukemia virus carrying a v-myc oncogene

Many retroviruses that carry oncogenes (acute transforming viruses) are generally replication-defective and therefore require co-infection with a replication competent 'helper' retrovirus for infectivity. The helper virus provides the retroviral proteins necessary for particle production and infection. These include the envelope glycoproteins that specifically bind to cell surface receptors and mediate viral adsorption and entry. Thus, a particular helper virus may influence the nature of disease induced by an oncogene-containing retrovirus due to tissue tropism of the helper. In a previous study, a replication-defective recombinant Moloney murine leukemia virus containing the v-myc oncogene was generated (M-MuLV(myc); Brightman B.K., Pattengale P.K., and Fan H., J Virol 60: 68-81, 1986). When M-MuLV(myc) was inoculated into mice using the non-pathogenic amphotropic murine leukemia virus (Am-MuLV 4070) as a helper, T- and B-lymphoblastic lymphomas resulted with the following two surface phenotypes, namely, (1) Thy 1.2+, B220- and (2) Thy 1.2-, B220+. Thy 1.2 surface antigen is characteristic of cells of the lymphoid lineage, whereas B220 surface antigen is characteristic of cells of the B-lymphoid lineage. In these experiments, to assess the influence of the helper virus on the disease specificity of M-MuLV(myc), two weakly pathogenic ecotropic helper MuLVs that interact with different cell surface receptors than Am-MuLV (Mo+PyF101 and AKV MuLV) were used to pseudotype M-MuLV(myc). In both cases, when inoculated into mice, these pseudotypes induced only T-lymphoblastic lymphoma. These results indicate that for M-MuLV(myc) the types of the tumors induced are influenced by the helper virus utilized, and they suggest that different lymphoid cells may express different levels of retroviral receptors.

Induction of Tax i expression in MT-4 cells by 5-azacytidine leads to protein binding in the HTLV-1 LTR in vivo

The Tax I trans-activator protein of the human T-cell leukemia virus I (HTLV-I) enhances viral gene expression through enhancer sequences in the viral LTR. These sequences consist of three imperfect 21-bp repeats (TRE-1) and a region between the promoter central and promoter proximal TRE-1 (known as TRE-2). We have previously described the in vivo footprint of the HTLV-I TRE-1s and TRE-2 in two HTLV-I-infected cell lines, MT-2 and MT-4. MT-2 is a high-level producer of virus and shows significant DNA-protein interactions within the TRE-1s and TRE-2. In contrast, the proviral DNA in MT-4 cells is heavily methylated and produces no detectable virus. In this report, we describe the footprints of the TRE-1s and TRE-2 in MT-4 cells that were induced to express high levels of viral proteins by treatment with 5-azacytidine, a potent inhibitor of methylation. The footprints of the TRE-1s in 5-azacytidine-treated MT-4 cells were virtually identical to those observed in MT-2 cells. In contrast, the footprints within the TRE-2 region of 5-azacytidine-treated MT-4 cells did not resemble those in either MT-2 or MT-4 cells.

Purification of Moloney murine leukemia virus chromatin from infected cells by an affinity method

Our goal was to develop a system to study proteins that associate in vivo with the Moloney murine leukemia virus (M-MuLV) enhancer elements by the isolation of intact proviral chromatin. The M-MuLV long terminal repeats (LTRs) contain tandemly repeated transcriptional enhancer sequences consisting of smaller motifs that bind cellular DNA-binding proteins implicated in transcriptional regulation. The M-MuLV enhancers are also important for disease specificity and latency of disease induction. To enrich for proviral chromatin containing M-MuLV LTR sequences, an affinity purification scheme was employed that relies on the affinity of bacterial Lac repressor protein for Lac operator (LacO) DNA sequences. An infectious M-MuLV recombinant was constructed that contains bacterial LacO sequences inserted into a nonessential region downstream from the 5' LTR of the virus (M-MuLV-LacO). Nuclei from M-MuLV-LacO-infected cells were digested with PvuII (which will liberate an LTR fragment containing LacO sequences), and digested chromatin was leached from the nuclei in hypotonic buffer. M-MuLV-LacO chromatin was then recovered by binding to an affinity matrix consisting of a beta-galactosidase-Lac repressor fusion protein anchored to acrylamide beads by an anti-beta-galactosidase monoclonal antibody [7]. Specifically bound chromatin was eluted under physiological conditions by incubation with the galactose analog isopropyl-beta-D-thiogalactopyranoside. Southern blot analysis confirmed the specific enrichment of M-MuLV proviral chromatin by this method.

Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks

A method of dynamically assembling molecular building blocks - DycoBlock - has been proposed and tested by Liu et al. This method is based on multiple-copy stochastic dynamics simulation in the presence of a receptor molecule. In this method, a novel algorithm was used to dynamically assemble the molecular building blocks to form candidate compounds. Currently, some new improvements have been incorporated into DycoBlock to make it more efficient. In the new version of DycoBlock, the binding energy and solvent accessible surface area (SASA) can be used to screen the resulting compounds. A simple clustering algorithm based on molecular similarity was developed and used to classify the remaining compounds. The revised DycoBlock was tested by breaking SC-558 - a selective inhibitor of cyclooxygenase-2 (COX-2) - into building blocks and reassembling them in the active site of the enzyme. The accuracy of recovery grew to 58.8% while it was only 16.7% in the previous version. Then, thirty-three kinds of molecular building blocks were used in the design of novel inhibitors and the investigation of diversity. As a result, a total of 1441 compounds was generated with high diversity. After the first screening procedure, there remained 864 reasonable compounds. The results from clustering indicate that the structural motifs in the diarylheterocycle class of COX-2-selective inhibitors have been generated using the revised DycoBlock, and their binding modes were investigated.