OfftargetFinder: a web tool for species-specific RNAi design.

MOTIVATION: RNA interference (RNAi) technology is being developed as a weapon for pest insect control. To maximize the specificity that such an approach affords we have developed a bioinformatic web tool that searches the ever-growing arthropod transcriptome databases so that pest-specific RNAi sequences can be identified. This will help technology developers finesse the design of RNAi sequences and suggests which non-target species should be assessed in the risk assessment process. AVAILABILITY AND IMPLEMENTATION: http://rnai.specifly.org CONTACT: crobin@unimelb.edu.au.

Safety, effectiveness and tolerance of buprenorphine-naloxone in the treatment of opioid dependence: results from a nationwide non-interventional study in routine care.

INTRODUCTION: Buprenorphine is well known in the treatment of opioid dependence. Despite a high safety profile and good tolerance buprenorphine has been subject to misuse and diversion. To reduce misuse the antagonist naloxone was added and the 4:1 combination of buprenorphine-naloxone was launched in Germany in March 2007. On the basis of the results from international clinical trials a non-interventional study was conducted to gather data on safety, effectiveness, retention and acceptability of buprenorphine-naloxone in the treatment of opioid dependent patients in routine care. METHODS: A nationwide multicentre 12-month prospective, non-interventional, post-marketing, surveillance study was carried out with 12 assessment points in N=384 opioid dependent patients currently in maintenance treatment from N=69 general practitioners, clinics and outpatient clinics in Germany. RESULTS: N=337 data sets were eligible for analysis. The rates of patients with serious and non-serious adverse events were low with 1.2% and 17.5%, respectively. No deaths occurred during the observational period and only one hospitalization was documented. Concomitant drug use decreased for all illicit substances. Mental health and quality of life measured with standardized self-assessment questionnaires improved significantly. The 12-month retention rate was 57.1%. Of the n=181 patients still in treatment at the end of the observation period, 96.7% continued treatment with buprenorphine-naloxone. CONCLUSION: The findings of the non-interventional study indicate high effectiveness and safety of buprenorphine-naloxone in the treatment of opioid dependence. The medication was well accepted by opioid dependent patients in long-term substitution treatment with substantial reductions of concomitant drug use and measurable improvement in quality of life.

Efficacy, adherence and tolerability of once daily tenofovir DF-containing antiretroviral therapy in former injecting drug users with HIV-1 receiving opiate treatment: results of a 48-week open-label study.

OBJECTIVE: To assess efficacy, adherence and tolerability of once daily antiretroviral therapy containing tenofovir disoproxil fumarate (DF) 300 mg in HIV-1-infected former injecting drug users receiving opiate treatment (IVDU). METHODS: European, 48-week, open-label, single-arm, multicenter study. Patients were either antiretroviral therapy-naive, restarting therapy after treatment discontinuation without prior virological failure or switching from existing stable treatment. RESULTS: Sixty-seven patients were enrolled in the study and 41 patients completed treatment. In the primary analysis (intent-to-treat missing=failure) at week 48, 34% of patients (23/67; 95% CI: 23%-47%) had plasma HIV-1 RNA <50 copies/mL. Using an intent-to-treat missing=excluded approach, the week 48 proportion of patients with plasma HIV-1 RNA <50 copies/mL increased to 56% (23/41; 95% CI: 40%-72%). Mean (standard deviation) increase from baseline in CD4+ cell count at week 48 was 176 (242) cells/mm(3). Although self-reported adherence appeared high, there were high levels of missing data and adherence results should be treated with caution. No new safety issues were identified. CONCLUSIONS: Levels of missing data were high in this difficult-to-treat population, but potent antiretroviral suppression was achieved in a substantial proportion of HIV-infected IVDU-patients.

The influence of HAART on the efficacy and safety of pegylated interferon and ribavirin therapy for the treatment of chronic HCV infection in HIV-positive Individuals.

OBJECTIVE: This study was performed to investigate the impact of HAART versus no HAART and nucleoside free versus nucleoside containing HAART on the efficacy and safety of pegylated interferon and ribavirin therapy for the treatment of chronic HCV infection in HIV/HCV co-infected patients. In addition a control group of HCV mono-infected patients undergoing anti-HCV therapy was evaluated. METHODS: Multicenter, partially randomized, controlled clinical trial. HIV-negative and -positive patients with chronic HCV infection were treated with pegylated interferon alfa-2a and ribavirin (800 - 1200 mg/day) for 24 - 48 weeks in one of four treatment arms: HIV-negative (A), HIV-positive without HAART (B) and HIV-positive on HAART (C). Patients within arm C were randomized to receive open label either a nucleoside containing (C1) or a nucleoside free HAART (C2). RESULTS: 168 patients were available for analysis. By intent-to-treat analysis similar sustained virological response rates (SVR, negative HCV-RNA 24 weeks after the end of therapy) were observed comparing HIV-negative and -positive patients (54% vs. 54%, p = 1.000). Among HIV-positive patients SVR rates were similar between patients off and on HAART (57% vs. 52%, p = 0.708). Higher SVR rates were observed in patients on a nucleoside free HAART compared to patients on a nucleoside containing HAART, though confounding could not be ruled out and in the intent-to-treat analysis the difference was not statistically significant (64% vs. 46%, p = 0.209). CONCLUSIONS: Similar response rates for HCV therapy can be achieved in HIV-positive and -negative patients. Patients on nucleoside free HAART reached at least equal rates of sustained virological response compared to patients on standard HAART.

The maize rough sheath2 gene and leaf development programs in monocot and dicot plants.

Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.

Treatment during primary HIV infection does not lower viral set point but improves CD4 lymphocytes in an observational cohort.

OBJECTIVE: To investigate if early treatment of primary HIV-1 infection (PHI) reduces viral set point and/or increases CD4 lymphocytes. METHODS: Analysis of two prospective multi-centre PHI cohorts. HIV-1 RNA and CD4 lymphocytes in patients with transient treatment were compared to those in untreated patients. Time to CD4 lymphocyte decrease below 350/ microl after treatment stop or seroconversion was calculated using Kaplan-Meier and Cox-PH-regression analyses. RESULTS: 156 cases of PHI were included, of which 100 had received transient HAART (median treatment time 9.5 months) and 56 remained untreated. Median viral load (563000 cop/ml vs 240000 cop/ml; p<0.001) and median CD4 lymphocyte (449/ microl vs. 613/ microl; p<0.01) differed significantly between treated and untreated patients. Median viral load was 38056 copies/ml in treated patients (12 months after treatment stop) and 52880 copies/ml in untreated patients (12 months after seroconversion; ns). Median CD4 lymphocyte change was +60/ microl vs. -86/ microl (p = 0.01). Median time until CD4 lymphocytes decreased to <350/ microl (including all patients with CD4 lymphocytes <500/ microl during seroconversion) was 20.7 months in treated patients after treatment stop and 8.3 months in untreated patents after seroconversion (p<0.01). Cox-PH analyses adjusting for baseline VL, CD4 lymphocytes, stage of early infection and symptoms confirmed these differences. CONCLUSIONS: Treatment during PHI did not lower viral set point. However, patients treated during seroconversion had an increase in CD4 lymphocytes, whereas untreated patients experienced a decrease in CD4 lymphocytes. Time until reaching CD4 lymphocytes <350/ microl was significantly shorter in untreated than in treated patients including patients with CD4 lymphocytes <500/ microl during seroconversion.

Self-incompatibility in flowering plants.

Fertilization in flowering plants begins with a pollen grain bearing the male gametes landing on the female stigma. Several mechanisms enable the stigma to discriminate between the different types of pollen that it may receive, of which the best studied is self-incompatibility. The molecules that regulate self-incompatibility are well characterized in two plant families, the Solanaceae and Brassicaceae. This list has recently been extended to include candidates for self-incompatibility molecules from the Rosaceae, Papaveraceae and Poaceae. The information provided by the sequences of these molecules gives insight into the mechanisms and evolution of self-incompatibility in the different families of flowering plants.

Plant development: YABBYs claw to the fore.

The YABBY gene family was identified recently by homology to CRABS CLAW, a gene involved in carpel and nectary development in Arabidopsis. Several of the transcription factors encoded by the YABBY genes appear to have conserved roles in specifying abaxial cell fate in leaves, floral organs and ovules.

A molecular description of mutations affecting the pollen component of the Nicotiana alata S locus.

Mutations affecting the self-incompatibility response of Nicotiana alata were generated by irradiation. Mutants in the M1 generation were selected on the basis of pollen tube growth through an otherwise incompatible pistil. Twelve of the 18 M1 plants obtained from the mutagenesis screen were self-compatible. Eleven self-compatible plants had mutations affecting only the pollen function of the S locus (pollen-part mutants). The remaining self-compatible plant had a mutation affecting only the style function of the S locus (style-part mutant). Cytological examination of the pollen-part mutant plants revealed that 8 had an extra chromosome (2n + 1) and 3 did not. The pollen-part mutation in 7 M1 plants was followed in a series of crosses. DNA blot analysis using probes for S-RNase genes (encoding the style function of the S locus) indicated that the pollen-part mutation was associated with an extra S allele in 4 M1 plants. In 3 of these plants, the extra S allele was located on the additional chromosome. There was no evidence of an extra S allele in the 3 remaining M1 plants. The breakdown of self-incompatibility in plants with an extra S allele is discussed with reference to current models of the molecular basis of self-incompatibility.

[HIV and drug users: current trends]. / HIV-therapie und Drogensubstitution am besten aus einer Hand. Therapiebesonderheiten bei Drogenabhängigen.

Despite an extensive addiction treatment and rehabilitation system for heroin addicts, inadequate infectious disease care still prevails for this group of patients. The reasons are structural in nature since both of the required medical disciplines (addiction medicine and infectious diseases epidemiology) are rarely found at one treatment location. Appropriate interdisciplinary cooperation must first be established. In a specialized heroin addiction treatment setting, patient compliance isjust as good as in other risk groups. Prerequisites for this good compliance are: Elimination of social and psychiatric disruptive factors, the selection of a medication regimen that takes secondary diseases and concomitant medication into consideration and the employment of once-daily treatment regimens or simple regimens with twice-daily dosages.

German-Austrian recommendations for the antiretroviral therapy of HIV-infection (status May 2004).

The availability and application of effective antiretroviral combination therapies have now almost become routine. More than 20 antiretroviral substances in four classes have been approved. Although an almost incalculable number of combinations can be conceived, it must be stressed, that only a small number of the theoretically possible combinations are actually applicable. As a result of the broad therapeutic armamentarium, HIV infection can be better treated. However, the decisions to start, monitor and change therapy have become even more difficult because the indication for treatment, the selection of the most suitable therapy for an individual, the information and counselling of the patient, and the monitoring of the success of treatment all demand a high level of knowledge and experience. This guideline evaluates the indication and selection of the initial antiretroviral therapy for HIV infection.

Diagnostics and treatment of HIV-discordant couples who wish to have children.

Over the last years the reality surrounding HIV-infection has undergone a considerable change with regard to the life expectancy of patients, and the plans they can make for their lives. Because the majority of the HIV positive population is of reproductive age, one of these plans might be to have children, often as an expression of a fulfilled partnership. The need for medical support to realize this wish, however, is often confronted with ethical, medical or forensic restraints. For this reason, interdisciplinary recommendations have now been developed--for the first time on a global basis--which aim to provide guidelines for practitioners in this complicated area.

Differences between the course of the drug addict's HIV infection and that of other HIV-infected patients.

Drug addicts have, in general, a less complicated course of HIV infection than homosexual HIV patients. They show fewer opportunistic infections and tumors. But this advantage is lost by unnecessary complications due to their psychic disorders. Their non-compliance and concealment of signs of disease lead to worse outcomes of infections, which could be well-treated or prevented.

[Prevention of HIV in injecting drug addicts. What has been done - what could be better?]. / HIV-Prävention bei Drogenkonsumenten. Was haben wir gemacht - was könnten wir besser machen?

Efficient prevention of HIV in drug users has had to overcome major political opposition in the last decade. Even today many evidence-based measures for the prevention of infections in drug users are still not being applied. Only a few preventive approaches are broadly carried out in the GFR: methadone maintenance performed by general practitioners, antiretroviral therapy and information about safer use given by AIDS- and drug-consultants and syringeexchange by pharmacies and at special institutions. In contrast, injection room facilities, street workers council, vaccination programs and low threshold medical treatment are only implemented in isolated cases. Nevertheless, HIV prevalence among drug users has been reduced successfully and the rate of new infections has decreased from 13.2% in 1994 to 9% in 2006. These strategies, however, do not seem to have any effect on the spread of hepatitis C among drug users. Here we still face a prevalence of 45-70%. Therefore, future research should focus on preventive measures against HCV infection of drug users.

[Pain therapy in addicted patients]. / Schmerztherapie bei suchtmittelabhängigen Patienten.

Each individual is entitled to an adequate and sufficient pain therapy. However, only a few studies have examined the peculiarities of pain management in drug-dependent or formerly addicted patients. Any addiction is disadvantageous for a successful pain therapy, since some of the prescribed drugs may themselves cause addiction. Drug-dependent patients are often tolerant to opioids. Additionally, there is a risk of iatrogenic pain becoming chronic due to disregard for already known risk factors and comorbidities. However, a history of addiction should not prevent sufficient pain therapy, especially since there is no risk of addiction when the pain therapy employed is adequate for the pathophysiology involved. There are adequate pain therapies for addicted patients. The best results are achieved by taking into account the physiological and psychological peculiarities of drug-dependent patients. Importantly, this should be combined with a variety of different, optimized, multimodal therapeutic regimes, as well as with an interdisciplinary approach.

[Ambulatory medical treatment of drug dependent patients]. / Ambulante ärztliche Behandlung von Drogenabhängigen.

The treatment and counseling of drug addicts increasingly comes under the responsibility of family physicians. Since the onset of the AIDS epidemic this applies in particular to the methadone treatment of chronically ill heroin addicts. Medical education concerning the treatment of addiction is insufficient. Unprofessional dealing with drug addicts may easily result in serious obstruction of the relation between physician and patient. Thus it endangers the success of treatment. Basic guidelines of interaction, possibilities of abstinence therapy as well as harm reducing strategies are presented.

A relic S-RNase is expressed in the styles of self-compatible Nicotiana sylvestris.

We surveyed ribonuclease activity in the styles of Nicotiana spp. and found little or no activity in self-compatible species and in a self-compatible accession of a self-incompatible species. All self-incompatible species had high levels of ribonuclease activity in their style. Interestingly, one self-compatible species, N. sylvestris, had a level of stylar ribonuclease activity comparable to that of some self-incompatible Nicotiana species. A ribonuclease with biochemical properties similar to those of the self-incompatibility (S-)RNases of N. alata was purified from N. sylvestris styles. The N-terminal sequence of this protein was used to confirm the identity of a cDNA corresponding to the stylar RNase. The amino acid sequence deduced from the cDNA was related to those of the S-RNases and included the five conserved regions characteristic of these proteins. It appears that the N. sylvestris RNase may have evolved from the S-RNases and is an example of a 'relic S-RNase'. A number of features distinguish the N. sylvestris RNase from the S-RNases, and the role these may have played in the presumed loss of the self-incompatibility response during the evolution of this species are discussed.

Genetic analysis of Nicotiana pollen-part mutants is consistent with the presence of an S-ribonuclease inhibitor at the S locus.

Self-incompatibility (SI) is a genetic mechanism that restricts inbreeding in flowering plants. In the nightshade family (Solanaceae) SI is controlled by a single multiallelic S locus. Pollen rejection in this system requires the interaction of two S locus products: a stylar (S)-RNase and its pollen counterpart (pollen S). pollen S has not yet been cloned. Our understanding of how this gene functions comes from studies of plants with mutations that affect the pollen but not the stylar SI response (pollen-part mutations). These mutations are frequently associated with duplicated S alleles, but the absence of an obvious additional allele in some plants suggests pollen S can also be deleted. We studied Nicotiana alata plants with an additional S allele and show that duplication causes a pollen-part mutation in several different genetic backgrounds. Inheritance of the duplication was consistent with a competitive interaction model in which any two nonmatching S alleles cause a breakdown of SI when present in the same pollen grain. We also examined plants with presumed deletions of pollen S and found that they instead have duplications that included pollen S but not the S-RNase gene. This finding is consistent with a bipartite structure for the S locus. The absence of pollen S deletions in this study and perhaps other studies suggests that pollen S might be required for pollen viability, possibly because its product acts as an S-RNase inhibitor.

Development and validation of adolescent-perceived microsystem scales: social support, daily hassles, and involvement.

Developed and validated instruments for urban and culturally diverse adolescents to assess their self-reported transactions with family, peer, school, and neighborhood microsystems for the constructs of social support, daily hassles, and involvement. The sample of 998 youth were from schools in three Eastern cities with high percentages of economically disadvantaged youth. Data were collected before and after the transition to junior high school or to senior high school. Blacks constituted 26%, whites 26%, and Latinos 37% of the sample. Factor analyses confirmed and enhanced the hypothesized four-factor microsystem factor structure for support, hassles, and involvement; internal consistency and stability coefficients were consistent with these structures. In general, the microsystem factors were common across gender, ethnicity, and age. However, when group differences did occur on these demographic variables, they tended to validate the salience of microsystem specificity. In contrast to the total scores, the microsystem-specific factors yielded more meaningful and differential information with regard to demographic differences and the mediating processes across a school transition.