Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).

BACKGROUND: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. RESULTS: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. CONCLUSIONS: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.

Several well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step, highly discordant genes within genomic blocks (putative paralogs) are identified and excluded from the data set and, in the second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the principal tree(s) that make up the species tree/network without violating the underlying model. The potential of the approach is evaluated on simulated data derived from a species network composed of nine species, of which one is of hybrid origin, and displaying a single-gene duplication that leads to paralogous comparisons. We apply our method to an empirical set of 12 genes from 7 species sampled in the plant genus Medicago that display phylogenetic discordance. We identify the causes of the discordance and demonstrate that the Medicago orbicularis lineage experienced an episode of ancient hybridization. Our results show promise as a new way to explore phylogenetic sequence data that can significantly improve species tree inference in presence of hybridization and undetected paralogy or other causes leading to extremely discordant gene trees. [Coalescent simulation; gene tree; genomic location; hybridization; incomplete lineage sorting; paralogy; phylogenetic incongruence; principal tree; species tree.].

A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae).

Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species was formed through HHS by sampling eight nuclear loci and 22 individuals, with additional individuals from related species, using gene capture and Illumina sequencing. Phylogenetic inference and coalescent simulations were performed to infer the causes of gene tree incongruence. We found no evidence that phylogenetic differences among M. prostrata individuals were the result of HHS. Instead, an autopolyploid origin of tetraploids with introgression from tetraploids of the M. sativa complex is likely. We argue that tetraploid M. prostrata individuals constitute a new species, characterised by a partially non-overlapping distribution and distinctive alleles (from the M. sativa complex). No gene flow from tetraploid to diploid M. prostrata is apparent, suggesting partial reproductive isolation. Thus, speciation via autopolyploidy appears to have been reinforced by introgression. This raises the intriguing possibility that introgressed alleles may be responsible for the increased range exploited by tetraploid M. prostrata with respect to that of the diploids.

Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families.

Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus interactions complicate the means of inferring past genetic events. Genomic data have provided valuable information about the polyploid history of numerous species, but on their own fail to show whether related species, each with a polyploid past, share a particular polyploid event. A phylogenetic approach provides a powerful method to determine this but many processes may mislead investigators. These processes can affect individual gene trees, but most likely will not affect all genes, and almost certainly will not affect all genes in the same way. Thus, a multigene approach, which combines the large-scale aspect of genomics with the resolution of phylogenetics, has the power to overcome these difficulties and allow us to infer genomic events further into the past than would otherwise be possible. Previous work using synonymous distances among gene pairs within species has shown evidence for large-scale duplications in the legumes Glycine max and Medicago truncatula. We present a case study using 39 gene families, each with three or four members in G. max and the putative orthologues in M. truncatula, rooted using Arabidopsis thaliana. We tested whether the gene duplications in these legumes occurred separately in each lineage after their divergence (Hypothesis 1), or whether they share a round of gene duplications (Hypothesis 2). Many more gene family topologies supported Hypothesis 2 over Hypothesis 1 (11 and 2, respectively), even after synonymous distance analysis revealed that some topologies were providing misleading results. Only ca. 33% of genes examined support either hypothesis, which strongly suggests that single gene family approaches may be insufficient when studying ancient events with nuclear DNA. Our results suggest that G. max and M. truncatula, along with approximately 7000 other legume species from the same clade, share an ancient round of gene duplications, either due to polyploidy or to some other process.

Paralogy and orthology in the MALVACEAE rpb2 gene family: investigation of gene duplication in hibiscus.

A sample of the second largest subunit of low-copy nuclear RNA polymerase II (rpb2) sequences from Malvaceae subfamily Malvoideae suggests that rpb2 has been duplicated early in the subfamily's history. Hibiscus and related taxa possess two rpb2 genes, both of which produce congruent phylogenetic patterns that are largely concordant with cpDNA topologies. No evidence of functional divergence or disruption was found among duplicated copies, suggesting that long-term maintenance of duplicated copies of rpb2 is usual in this lineage. Therefore, this gene may be suitable for the potential diagnosis of relatively old polyploid events. One probable pseudogene was found in Radyera farragei and a single chimeric sequence was recovered from Howittia trilocularis, suggesting that the rpb2 locus is not as prone to evolutionary processes that can confound phylogenetic inferences based on nDNA sequences. The pattern of relationships among rpb2 sequences, coupled with chromosome number information and Southern hybridization data, suggests that an early polyploid event was not the cause of the duplication, despite independent evidence of paleopolyploidy in some members of Malvoideae. Rpb2 exons and introns together are suitable for phylogenetic analysis, producing well-resolved and well-supported results that were robust to model permutation and congruent with previous studies of subfamily Malvoideae using cpDNA characters.

[Treatment of interdigital tinea pedis]. / Behandlung der Tinea pedis vom interdigitalen Typ. Systematischer Review.

BACKGROUND AND OBJECTIVE: Local antimycotic therapy of interdigital tinea pedis is widely accepted and efficacious. In Germany at present, the azoles and allylamines--part from the hydroxypyridone derivative ciclopiroxolamine--are the pharmacological agents applied most often. This study focuses on the efficacy of topical therapeutic options in Germany, by regarding the mycological and clinical cure rates of interdigital tinea pedis. METHODS: Only randomised, double-blind and controlled clinical trials of tinea pedis therapy were selected for the evaluation. Microbiological culture and microscopic information were indispensable criteria for the clinical diagnoses. RESULTS: The data from 40 randomised clinical trials of azoles and allylamines were included in the analysis. The comparison of azoles with the placebo revealed mycological cure rates between 60 - 91 % (placebo 10 - 67 %) and clinical cure rates between 64 - 95 % (placebo 10 - 63 %). Placebo-controlled trials of allylamines (naftifine and terbinafine) indicated mycological cure rates between 62 - 100 % (placebo 10 - 45 %) and clinical cure rates between 66 - 86 % (placebo 4 - 44 %). Both the azoles and the allylamines were significantly superior to the placebo. Comparative studies between azoles and allylamines occasionally indicated the significantly superior cure rates of allylamines (especially terbinafine). The high cure rates of terbinafine could be detected after therapy duration of merely one week, whereas the azoles have to be applied for four weeks before good efficacy was reached. CONCLUSION: In several trials the allylamines--especially terbinafine--proved superior to the azoles. This may be explained by the fungicidal mode of action of the allylamines and the favourable pharmacokinetic characteristics of terbinafine, in contrast to the fungistatic mechanism of the azoles.

[Socioeconomic relevance of acute exacerbations of chronic bronchitis in the Federal Republic of Germany. A prospective cost of illness study]. / Zur sozioökonomischen Relevanz akuter Exazerbationen der chronischen Bronchitis in der Bundesrepublik Deutschland. Eine prospektive Krankheitskostenstudie.

BACKGROUND AND OBJECTIVE: Prospectively determined data on costs of chronic bronchitis were not yet available for the Federal Republic of Germany. The purpose of the burden-of-illness-study conducted in the Federal Republic of Germany from October 1996 to March 1998 was to calculate direct and indirect costs of chronic bronchitis as well as its acute exacerbations per patient and year. Furthermore, the health-related quality of life of the patients was determined. PATIENTS AND METHODS: The burden-of-illness-study was conducted as an open, not randomised surveillance study. The evaluation based on 785 patients (55.4% male, 44.2% female, 0.4% unknown; mean age 60 years) who were treated by 147 general practitioners. 755 patients could be included into the cost analysis. RESULTS: Per patient and year direct costs of chronic bronchitis amounted to DM 1112.27, the calculation of indirect costs resulted in DM 959.09. 41.4% of direct costs were due to drug acquisition, hospitalisation costs shared 31.6% and costs for physicians' fee amounted to 20.6%. The severity of chronic bronchitis revealed significantly different results in cost analysis: per patient, mild disease lead to direct costs of DM 387.86, moderate disease to DM 802.62 and severe disease to DM 2224.40. This result was caused by higher costs for drug acquisition and hospitalisation costs due to chronic bronchitis in higher stages of severity. Indirect costs were calculated by applying the human-capital-approach: 45.8% of indirect costs were due to time-off-work, nursing costs amounted to 23.7%. CONCLUSION: The costs of chronic bronchitis have a considerable impact on the total costs of the health care system of Germany.

In vitro activity of rilopirox against fluconazole-susceptible and fluconazole-resistant Candida isolates from patients with HIV infection.

The in vitro antifungal activity of the new hydroxypyridone antimycotic rilopirox has been evaluated against 38 fluconazole-susceptible and -resistant clinical isolates of Candida albicans together with other Candida species isolated from patients with human immunodeficiency virus (HIV) infection and oropharyngeal candidosis. Minimum inhibitory concentrations (MICs) of both rilopirox and fluconazole were measured by a microdilution method using high-resolution medium supplemented with asparagine and glucose at pH 7.0. In comparison, an agar dilution technique was carried out for susceptibility testing of the antifungal agents. Rilopirox was found to be able to inhibit growth of all clinical yeast isolates. The rilopirox MICs at which 50% and 90% of strains were inhibited (MIC50 and MIC90 respectively), as determined by the microdilution method, were 4 and 8 micrograms ml-1 respectively. The highest MIC values for rilopirox using microdilution and the agar dilution method were 32 or 25 micrograms ml-1 respectively. On the other hand, for fluconazole, the MIC50 and MIC90 achieved were 0.5 and 128 micrograms ml-1, respectively, which means that the MIC90 value of fluconazole was 16-fold higher than that of rilopirox. Using the agar dilution technique, the MIC values of rilopirox were in the range 0.006-25 micrograms ml-1 with a median of 3.12 micrograms ml-1. For fluconazole, the MIC90 value was four-fold higher than that for rilopirox, indicating a considerable proportion of yeast strains with high MICs of 100 micrograms ml-1, suggesting in vitro resistance to this azole antifungal. All strains with diminished fluconazole susceptibility were susceptible to rilopirox. Even Candida krusei and Candida glabrata exhibited good in vitro susceptibility to rilopirox. Therefore, this new antifungal agent may be used as an alternative not only in the treatment of vaginal candidosis, but also in oropharyngeal Candida infections, e.g. in AIDS patients.

[Analysis of 1983-1991 Leipzig University Dermatology Clinic observed cases of syphilis]. / Analyse der von 1983-1991 an der Universitäts-Hautklinik Leipzig beobachteten Syphilisfälle.

A total of 1380 patients with syphilis were diagnosed and treated from January 1983 to December 1991 at the Department of Dermatology and Venereology at Leipzig University in West Saxon, Federal Republic of Germany where the population is 1.4 million. The incidence of syphilis increased gradually from 1983 to 1989 and then decreased again. The number of recent cases of syphilis was almost twice as high as latent syphilis cases (63:37%). The vast majority of cases suffered from early syphilis. In almost half the source of infection was casual contacts (44%); in one-third it was a stable partners (30%); about 6% were homosexuals and about 4% were prostitutes. Among the primary syphilis cases multiple chancres were seen in 16%. In 31% of cases, the ulcus durum was extragenital. Among the secondary syphilis cases macular and maculopapular exanthema were the commonest features (51%), followed by palmoplantar syphilis (5%), condylomata lata (5%), angina specifica (3%) and papular exanthema (3%). However, in 30% of the cases multiple skin features were observed. Secondary syphilis with persistent chancres were seen in 12%. Five percent of the patients were suffering from the second to the fifth reinfection in their life, and again 5% of the syphilis cases were detected during pregnancy. Only two patients had an HIV infection, 10% suffered from gonorrhea and 10% from trichomoniasis, 12% from chlamydial infection, 4% from genital warts and 8% from herpes simplex genitalis at the same time. The therapy of choice was penicillin. In 0.3% an allergy to penicillin was observed.(ABSTRACT TRUNCATED AT 250 WORDS)