Open source drug discovery - A limited tutorial

Open science is a new concept for the practice of experimental laboratory-based research, such as drug discovery. The authors have recently gained experience in how to run such projects and here describe some straightforward steps others may wish to take towards more openness in their own research programmes. Existing and inexpensive online tools can solve many challenges, while some psychological barriers to the free sharing of all data and ideas are more substantia

A Recoding Method to Improve the Humoral Immune Response to an HIV DNA Vaccine

This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine

A Novel Synthetic Yeast for Enzymatic Biodigester Pretreatment

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these enzymes to degrade lignocellulosic biomass. We incorporated the following genes into yeast vectors: laccase, lignin peroxidase, and alpha-keto-reductase from Reticulitermes flavipes; versatile peroxidase from Colletotrichum fioriniae PJ7; manganese peroxide from Heterobasidion irregulare TC 32-1; and tyrosinase from Agaricus bisporus. These vectors code for fusion proteins with yeast secretion tags at the end of each enzyme gene, fluorescent protein tags at the beginning, as well as standardized restriction sites for synthetic biology manipulation. Furthermore, we designed an additional vector to contain our genetically modified yeast using an oxygen-repressed killswitch. We expect that transformants with our construct will be able to secrete said enzymes and contribute to lignin degradation if added to a biomass slurry. Future studies may focus on constructing a prototype bioreactor system and optimizing which combination of enzymes lead to the most efficient biofuel production

The influence of age on the female/male ratio of treated incidence rates in depression

BACKGROUND: Poor data exist on the influence of psychosocial variables on the female/male ratio of depression because of the small number of cases and the resulting limited numbers of variables available for investigation. For this investigation a large number of first admitted depressed patients (N = 2599) was available which offered the unique opportunity to calculate age specific sex ratios for different marital and employment status categories. METHODS: Age and sex specific population based depression rates were calculated for first ever admissions for single year intervals. Moving averages with interpolated corrections for marginal values in the age distribution were employed. RESULTS: For the total group the female/male ratio of depression showed an inverted U-shape over the life-cycle. This pattern was influenced by the group of married persons, which showed a sex-ratio of 3:1 between the age of 30–50, but ratios of around 1:1 at younger and older ages. For not married persons the female/male ratio was already around 2:1 at the age of 18 and rose to 2.5:1 in mid-life and declined to 1 at around 55. The almost parallel decline of depression rates in employed men and women resulted in a female/male ratio of about 2:1 from age 18 to age 50 and became 1 after the age of 60. The female/male ratio among the not employed was about 1, in mid-life it became negative. CONCLUSIONS: Our analyses show that the gender-gap in first admitted depressed patients is age dependent and that psychosocial factors modify the sex ratio

Gender and sexual orientation differences in cognition across adulthood : age is kinder to women than to men regardless of sexual orientation

Despite some evidence of greater age-related deterioration of the brain in males than in females, gender differences in rates of cognitive aging have proved inconsistent. The present study employed web-based methodology to collect data from people aged 20-65 years (109,612 men; 88,509 women). As expected, men outperformed women on tests of mental rotation and line angle judgment, whereas women outperformed men on tests of category fluency and object location memory. Performance on all tests declined with age but significantly more so for men than for women. Heterosexuals of each gender generally outperformed bisexuals and homosexuals on tests where that gender was superior; however, there were no clear interactions between age and sexual orientation for either gender. At least for these particular tests from young adulthood to retirement, age is kinder to women than to men, but treats heterosexuals, bisexuals, and homosexuals just the same

Toward the Assessment of Food Toxicity for Celiac Patients: Characterization of Monoclonal Antibodies to a Main Immunogenic Gluten Peptide

13 pages, 8 figures.-- PMID: 18509534 [PubMed].-- PMCID: PMC2386552.[Background and Aims] Celiac disease is a permanent intolerance to gluten prolamins from wheat, barley, rye and, in some patients, oats. Partially digested gluten peptides produced in the digestive tract cause inflammation of the small intestine. High throughput, immune-based assays using monoclonal antibodies specific for these immunotoxic peptides would facilitate their detection in food and enable monitoring of their enzymatic detoxification. Two monoclonal antibodies, G12 and A1, were developed against a highly immunotoxic 33-mer peptide. The potential of each antibody for quantifying food toxicity for celiac patients was studied.[Methods] Epitope preferences of G12 and A1 antibodies were determined by ELISA with gluten-derived peptide variants of recombinant, synthetic or enzymatic origin.[Results] The recognition sequences of G12 and A1 antibodies were hexameric and heptameric epitopes, respectively. Although G12 affinity for the 33-mer was superior to A1, the sensitivity for gluten detection was higher for A1. This observation correlated to the higher number of A1 epitopes found in prolamins than G12 epitopes. Activation of T cell from gluten digested by glutenases decreased equivalently to the detection of intact peptides by A1 antibody. Peptide recognition of A1 included gliadin peptides involved in the both the adaptive and innate immunological response in celiac disease.[Conclusions] The sensitivity and epitope preferences of the A1 antibody resulted to be useful to detect gluten relevant peptides to infer the potential toxicity of food for celiac patients as well as to monitor peptide modifications by transglutaminase 2 or glutenases.This work was supported by the Asociación de Celiacos de Madrid (to Carolina Sousa), by the CTA (Corporación Tecnológica de Andalucía) and IDEA (Agencia de Innovación y Desarrollo de Andalucía) (to Angel Cebolla) and by grants BFU2007-64999 from Plan Nacional de Investigación científica, Desarrollo e Innovación tecnológica (Miniterio de Educación y Ciencia) and RICET-RD06/0021-0014, Spain (to Manuel C. López). Belén Morón was supported by a fellowship from Consejo Andaluz de Colegios Oficiales de Farmacéuticos.Peer reviewe

Bose-Einstein Correlations of Three Charged Pions in Hadronic Z^0 Decays

Bose-Einstein Correlations (BEC) of three identical charged pions were studied in 4 x 10^6 hadronic Z^0 decays recorded with the OPAL detector at LEP. The genuine three-pion correlations, corrected for the Coulomb effect, were separated from the known two-pion correlations by a new subtraction procedure. A significant genuine three-pion BEC enhancement near threshold was observed having an emitter source radius of r_3 = 0.580 +/- 0.004 (stat.) +/- 0.029 (syst.) fm and a strength of \lambda_3 = 0.504 +/- 0.010 (stat.) +/- 0.041 (syst.). The Coulomb correction was found to increase the \lambda_3 value by \~9% and to reduce r_3 by ~6%. The measured \lambda_3 corresponds to a value of 0.707 +/- 0.014 (stat.) +/- 0.078 (syst.) when one takes into account the three-pion sample purity. A relation between the two-pion and the three-pion source parameters is discussed.Comment: 19 pages, LaTeX, 5 eps figures included, accepted by Eur. Phys. J.

Phase I/pharmacokinetic study of CCI-779 in patients with recurrent malignant glioma on enzyme-inducing antiepileptic drugs

Objectives : CCI-779 is an ester of the immunosuppressive agent sirolimus (rapamycin) that causes cell-cycle arrest at G1 via inhibition of key signaling pathways resulting in inhibition of RNA translation. Antitumor activity has been demonstrated using cell lines and animal models of malignant glioma. Patients receiving enzyme-inducing anti-epileptic drugs (EIAEDs) can have altered metabolism of drugs like CCI-779 that are metabolized through the hepatic cytochrome P450 enzyme system. The objectives of this study were to determine the pharmacokinetic profile and the maximum tolerated dose of CCI-779 in patients with recurrent malignant gliioma taking EIAEDs. Study design: The starting dose of CCI-779 was 250 mg intravenously (IV) administered weekly on a continuous basis. Standard dose escalation was performed until the maximum tolerated dose was established. Toxicity was assessed using the National Cancer Institute common toxicity criteria. Results : Two of 6 patients treated at the second dose level of 330 mg sustained a dose-limiting toxicity: grade III stomatitis, grade 3 hypercholesterolemia, or grade 4 hypertriglyceridemia. The maximum tolerated dose was reached at 250 mg IV. Pharmacokinetic profiles were similar to those previously described, but the area under the whole blood concentration-time curve of rapamycin was 1.6 fold lower for patients on EIAEDs. Conclusions : The recommended phase II dose of CCI 779 for patients on enzyme-inducing antiepileptic drugs is 250 mg IV weekly. A phase II study is ongoing to determine the efficacy of this agent.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45250/1/10637_2004_Article_5273867.pd

Personality Traits, Self-Employment, and Professions

We investigate the effect of broad personality traits' - the Big Five - on an individua's decision to become self-employed. In particular, we test an overall indicator of the entrepreneurial personality. Since we find that the level of self-employment varies considerably across professions, we also perform the analysis for different types of professions, namely, those classified as being in the 'creative class' as compared to the noncreative class. The analysis is based on micro data for individuals of the German Socio Economic Panel (SOEP). We find a significant association between personality traits and the propensity be become self-employed. However, the strength of this link is fairly weak and differs across professions, indicating an important effect of an individual's profession on his or her decision to run an own business