[Molecular medicine: pathobiochemistry as the key to personalized treatment of inherited diseases]. / Molekulare Medizin: Pathobiochemie als Schlüssel zur personalisierten Therapie vererbter Krankheiten.

Genetic defects are often still regarded as a life-long fate, which one has to cope with. It is true that in many cases an inherited disposition may lead to a severe disease; however, it is also true that the number of genetic defects with a treatment option is continuously increasing and in some of them the onset of disease symptoms can even be totally prevented. Knowledge of the precise molecular pathomechanism is often the basis for a treatment concept. Genome-wide sequencing has tremendously increased the possibility to identify a genetic defect and its broad application has meanwhile made a decisive contribution in routine diagnostics. After identifying a genetic alteration, it is still necessary to investigate the pathobiochemical consequences on the cellular and systemic level. This can be a time-consuming process since not all functional consequences can be immediately recognized. In the case of metabolic defects the treatment strategy can either be a supplementation of missing products or a removal of toxic substrates. The residual function of affected pathways can also often be improved. Recently, the direct correction of the affected genetic defects has become a treatment option for a selected number of diseases. As the first symptoms of disease usually occur early in life, pediatrics has a pioneering role in developing treatment strategies.

Combined Campylobacter jejuni and Campylobacter coli Rapid Testing and Molecular Epidemiology in Conventional Broiler Flocks.

Campylobacter spp. are important causes of bacterial zoonosis, most often transmitted by contaminated poultry meat. From an epidemiological and risk assessment perspective, further knowledge should be obtained on Campylobacter prevalence and genotype distribution in primary production. Consequently, 15 Austrian broiler flocks were surveyed in summer for their thermophilic Campylobacter spp. contamination status. Chicken droppings, dust and drinking water samples were collected from each flock at three separate sampling periods. Isolates were confirmed by PCR and subtyped. We also compared three alternative methods (culture-based enrichment in Bolton broth, culture-independent real-time PCR and a lateral-flow test) for their applicability in chicken droppings. Twelve flocks were found to be positive for thermophilic Campylobacter spp. during the entire sampling period. Seven flocks (46.6%) were contaminated with both, C. jejuni and C. coli, five flocks harboured solely one species. We observed to a majority flock-specific C. jejuni and C. coli genotypes, which dominated the respective flock. Flocks within a distance <2 km shared the same C. jejuni genotypes indicating a cross-contamination event via the environment or personnel vectors. Multilocus sequence typing (MLST) of C. jejuni revealed that the majority of isolates were assigned to globally distributed clonal complexes or had a strong link to the human interface (CC ST-446 and ST4373). The combination of techniques poses an advantage over risk assessment studies based on cultures alone, as, in the case of Campylobacter, occurrence of a high variety of genotypes might be present among a broiler flock. We suggest applying the lateral-flow test under field conditions to identify 'high-shedding' broiler flocks at the farm level. Consequently, poultry farmers and veterinarians could improve hygiene measurements and direct sanitation activities, especially during the thinning period. Ultimately, real-time PCR could be applied to quantify Campylobacter spp. directly from chicken droppings and avoid non-interpretable results achieved by culture-dependent methods.

Economic comparison of the monitoring programmes for bluetongue vectors in Austria and Switzerland.

With the bluetongue virus serotype 8 (BTV-8) outbreak in 2006, vector monitoring programmes (according to EU regulation 1266/2007) were implemented by European countries to obtain information on the spatial distribution of vectors and the vector-free period. This study investigates the vector monitoring programmes in Austria and Switzerland by performing a retrospective cost analysis for the period 2006-2010. Two types of costs were distinguished: costs financed directly via the national bluetongue programmes and costs contributed in-kind by the responsible institutions and agricultural holdings. The total net costs of the monitoring programme in Austria amounted to €1,415,000, whereby in Switzerland the costs were valued at €94,000. Both countries followed the legislation complying with requirements, but differed in regard to sampling frequency, number of trap sites and sampling strategy. Furthermore, the surface area of Austria is twice the area of Switzerland although the number of ruminants is almost the same in both countries. Thus, for comparison, the costs were normalised with regard to the sampling frequency and the number of trap sites. Resulting costs per trap sample comprised €164 for Austria and €48 for Switzerland. In both countries, around 50 per cent of the total costs can be attributed to payments in-kind. The benefit of this study is twofold: first, veterinary authorities may use the results to improve the economic efficiency of future vector monitoring programmes. Second, the analysis of the payment in-kind contribution is of great importance to public authorities as it makes the available resources visible and demonstrates how they have been used.

KLF2 mutation is the most frequent somatic change in splenic marginal zone lymphoma and identifies a subset with distinct genotype.

To characterise the genetics of splenic marginal zone lymphoma (SMZL), we performed whole exome sequencing of 16 cases and identified novel recurrent inactivating mutations in Kruppel-like factor 2 (KLF2), a gene whose deficiency was previously shown to cause splenic marginal zone hyperplasia in mice. KLF2 mutation was found in 40 (42%) of 96 SMZLs, but rarely in other B-cell lymphomas. The majority of KLF2 mutations were frameshift indels or nonsense changes, with missense mutations clustered in the C-terminal zinc finger domains. Functional assays showed that these mutations inactivated the ability of KLF2 to suppress NF-κB activation by TLR, BCR, BAFFR and TNFR signalling. Further extensive investigations revealed common and distinct genetic changes between SMZL with and without KLF2 mutation. IGHV1-2 rearrangement and 7q deletion were primarily seen in SMZL with KLF2 mutation, while MYD88 and TP53 mutations were nearly exclusively found in those without KLF2 mutation. NOTCH2, TRAF3, TNFAIP3 and CARD11 mutations were observed in SMZL both with and without KLF2 mutation. Taken together, KLF2 mutation is the most common genetic change in SMZL and identifies a subset with a distinct genotype characterised by multi-genetic changes. These different genetic changes may deregulate various signalling pathways and generate cooperative oncogenic properties, thereby contributing to lymphomagenesis.

Monitoring of Usutu virus activity and spread by using dead bird surveillance in Austria, 2003-2005.

Usutu virus has been causing avian mortality in Austria since its emergence in 2001. Between 2003 and 2005 a total of 504 dead birds were examined by reverse-transcriptase polymerase chain reaction and immunohistochemistry for the presence of Usutu virus nucleic acid and antigen, respectively. In 2003, 92 birds (out of 177 birds) belonging to five different species were positive, while in 2004, only 11 (of 224) birds, and in 2005, 4 (of 103) birds proved positive, all of which were blackbirds (Turdus merula). Within the surveillance period the virus had spread from its initial area of emergence and circulation, the surroundings of Vienna, to large areas of the federal states of Lower Austria, Burgenland and Styria. However, the absolute numbers of Usutu virus associated avian deaths declined significantly during the course of the years. In addition, the proportion of birds with low amounts of virus in their tissues increased continuously, which may indicate developing herd immunity.

Atom fiber for omnidirectional guiding of cold neutral atoms.

We present an omnidirectional matter waveguide on an atom chip. The guide is based on a combination of two current-carrying wires and a bias field pointing perpendicular to the chip surface. Thermal atoms are guided for more than two complete turns along a 25-mm-long spiral path (with curve radii as short as 200 microm) at various atom-surface distances (35-450 microm). An extension of the scheme for the guiding of Bose-Einstein condensates is outlined.

Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements.

Each of the sequenced Sulfolobus genomes contains large numbers of putatively mobile elements, both IS elements (insertion sequence elements) and MITEs (miniature inverted-repeat transposable elements). There are 344 in the 3.0 Mb genome of Sulfolobus solfataricus P2 and 95 in the 2.7 Mb genome of Sulfolobus tokodaii. In the former they constitute more than 10% of the genome. Experimental data suggest that transposition of IS elements occurs frequently. Moreover, the gene order between the two organisms differs greatly, indicating that multiple rearrangements have occurred. This has also led to considerable speculation as to how the cells are viable. Recently, a third Sulfolobus genome was completed which contains no IS elements or MITEs. This enabled us to compare the gene orders of the three genomes and provide evidence for mobile element-induced rearrangements of sections of the genomes.

Trapping and manipulating neutral atoms with electrostatic fields.

We report on experiments with cold thermal (7)Li atoms confined in combined magnetic and electric potentials. A novel type of three-dimensional trap was formed by modulating a magnetic guide using electrostatic fields. We observed atoms trapped in a string of up to six individual such traps, a controlled transport of an atomic cloud over a distance of 400 microm, and a dynamic splitting of a single trap into a double well potential. Applications for quantum information processing are discussed.

Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses.

The double-stranded DNA genomes of the viruses SIRV1 and SIRV2, which infect the extremely thermophilic archaeon Sulfolobus and belong to the family Rudiviridae, were sequenced. They are linear, covalently closed at the ends, and 32,312 and 35,502 bp long, respectively, with an A+T content of 75%. The genomes of SIRV1 and SIRV2 carry inverted terminal repeats of 2029 and 1628 bp, respectively, which contain multiple direct repeats. SIRV1 and SIRV2 genomes contain 45 and 54 ORFs, respectively, of which 44 are homologous to one another. Their predicted functions include a DNA polymerase, a Holliday junction resolvase, and a dUTPase. The genomes consist of blocks with well-conserved sequences separated by nonconserved sequences. Recombination, gene duplication, horizontal gene transfer, and substitution of viral genes by homologous host genes have contributed to their evolution. The finding of head-to-head and tail-to-tail linked replicative intermediates suggests that the linear genomes replicate by the same mechanism as the similarly organized linear genomes of the eukaryal poxviruses, African swine fever virus and Chlorella viruses. SIRV1 and SIRV2 both contain motifs that resemble the binding sites for Holliday junction resolvases of eukaryal viruses and may use common mechanisms for resolution of replicative intermediates. The results suggest a common origin of the replication machineries of the archaeal rudiviruses and the above-mentioned eukaryal viruses. About 1/3 of the ORFs of each rudivirus have homologs in the Sulfolobus virus SIFV of the family Lipothrixviridae, indicating that the two viral families form a superfamily. The finding of inverted repeats of at least 0.8 kb at the termini of the linear genome of SIFV supports this inference.

Ecological risk assessment of endocrine disruptors.

The European Centre for Ecotoxicology and Toxicology of Chemicals proposes a tiered approach for the ecological risk assessment of endocrine disruptors, integrating exposure and hazard (effects) characterization. Exposure assessment for endocrine disruptors should direct specific tests for wildlife species, placing hazard data into a risk assessment context. Supplementing the suite of mammalian screens now under Organization for Economic Cooperation and Development (OECD) validation, high priority should be given to developing a fish screening assay for detecting endocrine activity in oviparous species. Taking into account both exposure characterization and alerts from endocrine screening, higher tier tests are also a priority for defining adverse effects. We propose that in vivo mammalian and fish assays provide a comprehensive screening battery for diverse hormonal functions (including androgen, estrogen, and thyroid hormone), whereas Amphibia should be considered at higher tiers if there are exposure concerns. Higher tier endocrine-disruptor testing should include fish development and fish reproduction tests, whereas a full life-cycle test could be subsequently used to refine aquatic risk assessments when necessary. For avian risk assessment, the new OECD Japanese quail reproduction test guideline provides a valuable basis for developing a test to detecting endocrine-mediated reproductive effects; this species could be used, where necessary, for an avian life-cycle test. For aquatic and terrestrial invertebrates, data from existing developmental and reproductive tests remain of high value for ecological risk assessment. High priority should be given to research into comparative endocrine physiology of invertebrates to support data extrapolation to this diverse fauna.

Epizootic podoknemidokoptiasis in American robins.

Epizootics of scaly leg disease caused by infection with the submacroscopic mite Knemidokoptes jamaicensis (Acari: Knemidokoptidae) in migratory American robins (Turdus migratorius) from a residential area of Tulsa (Oklahoma, USA) are documented during the winters (December through February) of 1993-94 and 1994-95. Estimates of 60 to > 80% of the birds in several different flights arriving in the area had lesions consistent with knemidokoptic mange. Epizootic occurrence of K. jamaicensis also is confirmed incidentally in American robins from Georgia (USA) in 1995 and 1998 and in Florida (USA) in 1991. These are the first confirmed epizootics of scaly leg attributed to infections with mites specifically identified as K. jamaicensis in North America. Severity of observed lesions in American robins ranged from scaly hyperkeratosis of the feet and legs to extensive proliferative lesions with loss of digits or the entire foot in some birds. Histologically, there was severe diffuse hyperkeratosis of the epidermis which contained numerous mites and multifocal aggregates of degranulating to degenerating eosinophilic heterophils; there was mild to severe superficial dermatitis with aggregates of eosinophilic heterophils and some mononuclear cells. Based on limited data from affected captive birds in Florida, we questioned the efficacy of ivermectin as an effective acaricide for knemidokoptiasis and propose that conditions associated with captivity may exacerbate transmission of this mite among caged birds. While knemidokoptic mange apparently can result in substantial host morbidity and possibly mortality, the ultimate impact of these epizootics on American robin populations presently is unknown.

Inbreeding and juvenile mortality in small populations of ungulates.

Juvenile mortality of inbred young was higher than that of noninbred young in 15 of 16 species of captive ungulates. In 19 of 25 individual females, belonging to ten species, a larger percentage of young died when the female was mated to a related male than when she was mated to an unrelated male.