Use of QSAR Global Models and Molecular Docking for Developing New Inhibitors of c-src Tyrosine Kinase.

A prototype of a family of at least nine members, cellular Src tyrosine kinase is a therapeutically interesting target because its inhibition might be of interest not only in a number of malignancies, but also in a diverse array of conditions, from neurodegenerative pathologies to certain viral infections. Computational methods in drug discovery are considerably cheaper than conventional methods and offer opportunities of screening very large numbers of compounds in conditions that would be simply impossible within the wet lab experimental settings. We explored the use of global quantitative structure-activity relationship (QSAR) models and molecular ligand docking in the discovery of new c-src tyrosine kinase inhibitors. Using a dataset of 1038 compounds from ChEMBL database, we developed over 350 QSAR classification models. A total of 49 models with reasonably good performance were selected and the models were assembled by stacking with a simple majority vote and used for the virtual screening of over 100,000 compounds. A total of 744 compounds were predicted by at least 50% of the QSAR models as active, 147 compounds were within the applicability domain and predicted by at least 75% of the models to be active. The latter 147 compounds were submitted to molecular ligand docking using AutoDock Vina and LeDock, and 89 were predicted to be active based on the energy of binding.

Variation in the cuticular hydrocarbons of the Mexican fruit fly Anastrepha ludens males between strains and age classes.

In this study cuticular hydrocarbons (CHCs) were characterized from wings of individual unmated males of different Anastrepha ludens (Loew) mass-reared strains of different ages (3 and 19-day-old): (a) a standard mass-reared colony (control), (b) a genetic sexing strain, (c) a selected strain, (d) a hybrid strain, and (e) wild males. We found that the hydrocarbon profiles in all males included two n-alkanes, five monomethyl alkanes, and two alkenes. CHCs ranged from C26 to C31 . The most prominent peaks were 2-methyloctacosane (2-Me-C28), n-nonacosene (C29:1), 2-methyltriacontane (2-Me-C30), and n-hentriacontene (C31:1). Significant variations in the CHC amounts of the mass-reared strains were observed from Day 9 and thereafter. Comparison of CHCs using multivariate and canonical analyses across ages and among mass-reared strains and wild males revealed qualitative and quantitative differences. The relative amounts of C29:1 and 2-Me-C30 were significantly higher across age groups in the mass-reared strains than those in the wild males. In contrast, amounts of n-nonacosane (C29) significantly increased in wild males as they aged. Through statistical analyses, we inferred that CHC amounts vary with age. Wild males differed significantly from the mass-reared strains in the amount of C29, and the genetic sexing strain Tap-7 had significantly higher values for 2-methylhexacosane (2-Me-C26). In contrast the selected and control strain differed from the other strains in amounts of C29:1 and 2-Me-C30. We suggest that differential profiles in hydrocarbon composition among the strains may be mainly due to environmental pressures.

Tests in mice of a dengue vaccine candidate made of chimeric Junin virus-like particles and conserved dengue virus envelope sequences.

Two new vaccine candidates against dengue virus (DENV) infection were generated by fusing the coding sequences of the self-budding Z protein from Junin virus (Z-JUNV) to those of two cryptic peptides (Z/DENV-P1 and Z/DENV-P2) conserved on the envelope protein of all serotypes of DENV. The capacity of these chimeras to generate virus-like particles (VLPs) and to induce virus-neutralizing antibodies in mice was determined. First, recombinant proteins that displayed reactivity with a Z-JUNV-specific serum by immunofluorescence were detected in HEK-293 cells transfected with each of the two plasmids and VLP formation was also observed by transmission electron microscopy. Next, we determined the presence of antibodies against the envelope peptides of DENV in the sera of immunized C57BL/6 mice. Results showed that those animals that received Z/DENV-P2 DNA coding sequences followed by a boost with DENV-P2 synthetic peptides elicited significant specific antibody titers (≥6.400). Finally, DENV plaque-reduction neutralization tests (PRNT) were performed. Although no significant protective effect was observed when using sera of Z/DENV-P1-immunized animals, antibodies raised against vaccine candidate Z/DENV-P2 (diluted 1:320) were able to reduce in over 50 % the number of viral plaques generated by infectious DENV particles. This reduction was comparable to that of the 4G2 DENV-specific monoclonal cross-reactive (all serotypes) neutralizing antibody. We conclude that Z-JUNV-VLP is a valid carrier to induce antibody-mediated immune responses in mice and that Z/DENV-P2 is not only immunogenic but also protective in vitro against infection of cells with DENV, deserving further studies. On the other side, DENV's fusion peptide-derived chimera Z/DENV-P1 did not display similar protective properties.

Development, genetic and cytogenetic analyses of genetic sexing strains of the Mexican fruit fly, Anastrepha ludens Loew (Diptera: Tephritidae).

BACKGROUND: Anastrepha ludens is among the pests that have a major impact on México's economy because it attacks fruits as citrus and mangoes. The Mexican Federal government uses integrated pest management to control A. ludens through the Programa Nacional Moscas de la Fruta [National Fruit Fly Program, SAGARPA-SENASICA]. One of the main components of this program is the sterile insect technique (SIT), which is used to control field populations of the pest by releasing sterile flies. RESULTS: To increase the efficiency of this technique, we have developed a genetic sexing strain (GSS) in which the sexing mechanism is based on a pupal colour dimorphism (brown-black) and is the result of a reciprocal translocation between the Y chromosome and the autosome bearing the black pupae (bp) locus. Ten strains producing wild-type (brown pupae) males and mutant (black pupae) females were isolated. Subsequent evaluations for several generations were performed in most of these strains. The translocation strain named Tapachula-7 showed minimal effect on survival and the best genetic stability of all ten strains. Genetic and cytogenetic analyses were performed using mitotic and polytene chromosomes and we succeeded to characterize the chromosomal structure of this reciprocal translocation and map the autosome breakpoint, despite the fact that the Y chromosome is not visible in polytene nuclei following standard staining. CONCLUSIONS: We show that mitotic and polytene chromosomes can be used in cytogenetic analyses towards the development of genetic control methods in this pest species. The present work is the first report of the construction of GSS of Anastrepha ludens, with potential use in a future Moscafrut operational program.

Wound Healing and Anti-Inflammatory Effects of a Newly Developed Ointment Containing Jujube Leaves Extract.

Ziziphus jujuba Mill. (jujube) is a well-known medicinal plant with pronounced wound healing properties. The present study aimed to establish the chemical composition of the lyophilized ethanolic extract from Romanian Ziziphus jujuba leaves and to evaluate the healing and anti-inflammatory properties of a newly developed lipophilic ointment containing 10% dried jujube leaves extract. The ultra-High-Performance Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry method was used, and 47 compounds were detected, among them the novel epicatechin and caffeic acid. The extract contains significant amounts of rutin (29.836 mg/g), quercetin (15.180 mg/g) and chlorogenic acid (350.96 µg/g). The lipophilic ointment has a slightly tolerable pH, between 5.41-5.42, and proved to be non-toxic in acute dermal irritation tests on New Zealand albino rabbits and after repeated administration on Wistar rats. The ointment also has a healing activity comparable to Cicatrizin (a pharmaceutical marketed product) on Wistar rats and a moderate anti-inflammatory action compared to the control group, but statistically insignificant compared to indomethacin in the rat-induced inflammation test by intraplantar administration of kaolin. The healing and anti-inflammatory properties of the tested ointment are due to phenolic acids and flavonoids content, less because of minor components as apocynin, scopoletin, and isofraxidin.

Molecular analysis of the virulence attenuation process in Junín virus vaccine genealogy.

The Junín virus strain Candid#1 was developed as a live attenuated vaccine for Argentine hemorrhagic fever. In this article, we report sequence information of the L and S RNAs of Junín virus Candid#1 and XJ#44 strains, and show the comparisons with the XJ13 wild-type strain and with other Junín virus strains, like Romero, IV4454 and MC2 strains, and other closely and distantly related arenaviruses. Comparisons of the nucleotide and amino acid sequences of all genes of three strains from the same vaccine genealogy, revealed different point mutations that could be associated with the attenuated phenotype. A 91% of the mutations found are consistent with a hypothesis of progressive attenuation of virulence from XJ13 to XJ#44 and to Candid#1; 39% of mutations were observed in XJ#44 and conserved in Candid#1, while another 52% of the mutations appeared only in Candid#1 strain. The remaining 9% corresponded to reverse mutations in the L gene. In summary, the present work shows a set of mutations that could be related to the virulence attenuation phenomenon. This information will serve as a starting point to study this biological phenomenon, provided that a reverse genetics system for Junín virus is developed to allow the generation of infectious virions with specific mutations.

Lymph node isolated tumor cells and micrometastases in pathological stage I non-small cell lung cancer: prognostic significance.

OBJECTIVE: To determine the prevalence and prognostic significance of lymph node micrometastases and isolated tumor cells (ITC) in patients submitted for radical resection for pathological stage I non-small cell lung cancer (NSCLC). METHODS: From January 1998 through December 2005, 87 consecutive pT1-2, pN0 NSCLC patients were enrolled. Surgical specimens were submitted to pathological routine examinations to define histotype, grade, stage, vascular invasion, necrosis and tumor proliferative index. A total of 694 regional lymph nodes were examined by means of serial sections stained with hematoxylin and eosin and labelled by immunohistochemistry (antibody AE1/AE3, DAKO). Relationships between these parameters and patients' prognosis were investigated. RESULTS: By histological examination, there were 36 squamous-cell carcinoma, 38 adenocarcinoma and 13 large-cell carcinoma. Micrometastases and ITC were detected in 19 lymph nodes (2.7%) of 14 patients (16%). Significant correlation was observed between micrometastases or ITC and adenocarcinoma (p=0.03) and the absence of necrosis (p=0.05). No relationship was demonstrated between micrometastases or ITC and T-status, vascular invasion or proliferative index (p>0.05). Median follow-up was 3.2 (range 0.25-8.6) years. Two- and 5-year disease-free survival was similar for patients with and without micrometastases or ITC (79% and 64% vs 81% and 64%, respectively). Recurrence occurred in three patients with (two local, 66%) and in 21 patients without micrometastases or ITC (three local, 14%) (p=0.186). By multivariate analysis only T-status was demonstrated to be a significant prognostic factor. DISCUSSION: Micrometastases or ITC to regional lymph nodes are demonstrated to be not a rare aspect of pathological stage I resected lung cancer. In our series, the presence of lymph nodes micrometastases does not affect long-term disease-free survival.

Acclimation to low level exposure of copper in Bufo arenarum embryos: linkage of effects to tissue residues.

The acclimation possibilities to copper in Bufo arenarum embryos was evaluated by means of three different low level copper exposure conditions during 14 days. By the end of the acclimation period the copper content in control embryos was 1.04 +/- 0.09 microg g(-1) (wet weight) while in all the acclimated embryos a reduction of about 25% of copper was found. Thus copper content could be considered as a biomarker of low level exposure conditions. Batches of 10 embryos (by triplicate) from each acclimation condition were challenged with three different toxic concentrations of copper. As a general pattern, the acclimation protocol to copper exerted a transient beneficial effect on the survival of the Bufo arenarum embryos. The acclimation phenomenon could be related to the selection of pollution tolerant organisms within an adaptive process and therefore the persistence of information within an ecological system following a toxicological stressor.

Synergistic effects of copper and butylic ester of 2,4-Dichlorophenoxyacetic acid (Esternon Ultra) on amphibian embryos.

Cu2+ and butylic ester of 2,4-Dichlorophenoxyacetic acid as Esternon Ultra (2,4-D) toxicity on Bufo arenarum embryos were evaluated by means of a short-term chronic toxicity test (AMPHITOX). The NOEC values for Cu and 2,4-D were 0.02 mg/L and 2 mg/L respectively. The toxicity profile curves for Cu and 2,4-D were reported. The interactions of the metal and the herbicide were evaluated by combined treatments with different concentrations of Cu and 2,4-D. Although in all cases, a synergistic effect between these chemicals was observed, the combination of concentrations exerting low level effects in isolated treatments resulted in more adverse embryonic survival. Considering that both products are extensively used in agroecosystems, this fact could be of concern for non target species like amphibians.

Sexual behavior and male volatile compounds in wild and mass-reared strains of the Mexican fruit fly Anastrepha ludens (Diptera: Tephritidae) held under different colony management regimes.

We compared the calling and mating behavior and volatile release of wild males Anastrepha ludens (Loew) with males from 4 mass-reared strains: (i) a standard mass-reared colony (control), (ii) a genetic sexing strain (Tap-7), (iii) a colony started from males selected on their survival and mating competitiveness abilities (selected), and (iv) a hybrid colony started by crossing wild males with control females. Selected and wild males were more competitive, achieving more matings under field cage conditions. Mass-reared strains showed higher percentages of pheromone calling males under field conditions except for Tap-7 males, which showed the highest percentages of pheromone calling males under laboratory cage conditions. For mature males of all strains, field-cage calling behavior increased during the last hour before sunset, with almost a 2 fold increase exhibited by wild males during the last half hour. The highest peak mating activity of the 4 mass-reared strains occurred 30 min earlier than for wild males. By means of solid phase microextraction (SPME) plus gas chromatography-mass spectrometry (GC-MS), the composition of volatiles released by males was analyzed and quantified. Wild males emitted significantly less amounts of (E,E)-α-farnesene but emitted significantly more amounts of (E,E)-suspensolide as they aged than mass-reared males. Within the 4 mass-reared strains, Tap-7 released significantly more amounts of (E,E)-α-farnesene and hybrid more of (E,E)-suspensolide. Differences in chemical composition could be explained by the intrinsic characteristics of the strains and the colony management regimes. Characterization of calling behavior and age changes of volatile composition between wild and mass-reared strains could explain the differences in mating competitiveness and may be useful for optimizing the sterile insect technique in A. ludens.

Correlation between adenoma and serrated lesion detection rates in an unselected outpatient population.

BACKGROUND: Serrated lesions have been recently implicated in colorectal carcinogenesis. Adenoma detection rate has been related with the risk of interval cancer. The correlation between adenoma detection rate and the serrated lesion detection rate is unclear. AIM: To assess the correlation between adenoma- and serrated lesion-detection rate in an unselected setting of outpatient colonoscopies. METHODS: Consecutive outpatients were retrospectively evaluated in one centre. Detection rates were expressed as number of patients with at least one serrated lesion or adenoma. For each endoscopist, correlation between adenoma detection rate and serrated lesions detection rate was calculated. RESULTS: Six endoscopists performed 2974 colonoscopies. 3240 lesions (59.5% adenomas, 37.8% serrated lesions, 0.5% cancer, and 2.3% other histology) were detected in 1228 procedures. Median adenoma detection rate and serrated lesions detection rate per endoscopist were 29.3% and 22.4%, respectively. A positive correlation between adenoma and serrated lesion detection rate (r(2)=0.78, p<0.001) was detected. CONCLUSIONS: Our study showed a statistically significant correlation between adenoma detection rate and serrated detection rate.

Differential toxicity and uptake of Diazinon on embryo-larval development of Rhinella arenarum.

Diazinon, an anti-cholinesterase organophosphate, is an extensively used pesticide. The main objective of this work was to assess the lethal and sublethal effects of Diazinon and its comparison with the uptake by embryos and larvae of the common South American toad Rhinella arenarum by means of standardized bioassays during acute (96 h), short-term chronic (168 h) and chronic (504 h) exposures. Toxicity resulted time- and stage-dependent, thus the lethal concentration 50 for 96 h, 168 h and 504 h were 27.2; 20.1 and 6.8 mg Diazinon L(-1) for embryos and 8, 6.7 and 1.9 mg Diazinon L(-1) for larvae. It is noteworthy the remarkable differences found in the concentration which caused lethality with those causing adverse effects on development such as malformations (teratogenic effects). Therefore, the teratogenic index from 144 h was greater than two; the main adverse effects were axial flexures, irregular borders, wavy tail, microcephaly, malformed mouth and adhesive structures, gut miscoiling, underdeveloped gills, cloacal edema, desquamation and severe hydropsy. Moreover, the characteristic sublethal effect of Diazinon on larvae was abnormal behavior related to neurotoxicity with a NOEC-168 h of 4.5 mg Diazinon L(-1). Diazinon contents in R. arenarum were time-dependent and significantly related to exposure concentration for both embryos and larvae. Diazinon contents were also stage-dependent, as it was up to 27 times higher for organisms exposed from blastula stage onwards than early larvae. These facts and the Hazard Quotients, a numerical expression of ecological risk, of 2.73, which is above USEPA's Level of Concern, showed the threat that Diazinon represents for R. arenarum populations.

Fitness cost implications of PhiC31-mediated site-specific integrations in target-site strains of the Mexican fruit fly, Anastrepha ludens (Diptera: Tephritidae).

Site-specific recombination technologies are powerful new tools for the manipulation of genomic DNA in insects that can improve transgenesis strategies such as targeting transgene insertions, allowing transgene cassette exchange and DNA mobilization for transgene stabilization. However, understanding the fitness cost implications of these manipulations for transgenic strain applications is critical. In this study independent piggyBac-mediated attP target-sites marked with DsRed were created in several genomic positions in the Mexican fruit fly, Anastrepha ludens. Two of these strains, one having an autosomal (attP_F7) and the other a Y-linked (attP_2-M6y) integration, exhibited fitness parameters (dynamic demography and sexual competitiveness) similar to wild type flies. These strains were thus selected for targeted insertion using, for the first time in mexfly, the phiC31-integrase recombination system to insert an additional EGFP-marked transgene to determine its effect on host strain fitness. Fitness tests showed that the integration event in the int_2-M6y recombinant strain had no significant effect, while the int_F7 recombinant strain exhibited significantly lower fitness relative to the original attP_F7 target-site host strain. These results indicate that while targeted transgene integrations can be achieved without an additional fitness cost, at some genomic positions insertion of additional DNA into a previously integrated transgene can have a significant negative effect. Thus, for targeted transgene insertions fitness costs must be evaluated both previous to and subsequent to new site-specific insertions in the target-site strain.

Pseudomembranous collagenous colitis with superimposed drug damage.

Pseudomembranous collagenous colitis is a rare pathological condition, not related to infectious agents, and characterized by thickening of the subepithelial collagen and formation of pseudomembranes. We report one such case, which responded to budesonide treatment after failures of previous approaches given, being unaware of the correct diagnosis.

Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides.

Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus (10 × 10(4) nucleotides), Baculovirus (0.9 × 10(5) to 1.8 × 10(5) bp), Lactobacillus sp. (1 × 10(6) to 2 × 10(6) bp), and Pseudomonas sp. (4 × 10(6) to 7 × 10(6) bp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members.

Primary vulvar Ewing's sarcoma/primitive neuroectodermal tumor in a post-menopausal woman: a case report.

Ewing's sarcomas/peripheral primitive neuroectodermal tumors (ES/pPNETs) are high-grade malignant neoplasms rarely found outside the skeletal system. Only 12 cases of vulvar ES/pPNET have so far been reported, all involving children or women of child-bearing age. We describe the case of a 52-year-old woman who was admitted to our hospital for the local excision of a 4cm vulvar mass, originally thought to be a Bartholin's gland cyst. It was subsequently found to consist of small round cells positive for anti-CD99 antibody, thus suggesting a diagnosis of ES/pPNET. The demonstration of EWSR1 gene translocations by means of fluorescent in situ hybridization excluded small-cell carcinoma, squamous cell carcinoma of the small type, Merkel cell carcinoma, and lymphoblastic lymphoma. After surgery, the patient received six cycles of polychemotherapy and radiotherapy; she is still alive and well after 1 year of follow-up. Our findings underline the crucial role of molecular biology techniques in the differential diagnosis of small round cell tumors in these unusual locations.