Differentiation of fungi using hybridization probes on the LightCycler(®)

The polymerase chain reaction is a powerful molecular tool for the detection and analysis of very small amounts of DNA. Today, hybridization probes are often used in real-time PCR for more sensitive and specific detection of pathogens and for determination of gene regulation or mutation analysis instead of intercalating dyes like SYBR Green. Here, we describe how to generate suitable primers and hybridization probes for the specific detection of fungal DNA. Furthermore, we show the advantages of hybridization probes using the LightCycler-PCR for the detection of different Candida spp. and Aspergillus spp. in patient blood samples. The methods used to develop such PCR assays will also be presented in the following protocol.

Measurement of finite-frequency current statistics in a single-electron transistor

Electron transport in nanoscale structures is strongly influenced by the Coulomb interaction that gives rise to correlations in the stream of charges and leaves clear fingerprints in the fluctuations of the electrical current. A complete understanding of the underlying physical processes requires measurements of the electrical fluctuations on all time and frequency scales, but experiments have so far been restricted to fixed frequency ranges, as broadband detection of current fluctuations is an inherently difficult experimental procedure. Here we demonstrate that the electrical fluctuations in a single-electron transistor can be accurately measured on all relevant frequencies using a nearby quantum point contact for on-chip real-time detection of the current pulses in the single-electron device. We have directly measured the frequency-dependent current statistics and, hereby, fully characterized the fundamental tunnelling processes in the single-electron transistor. Our experiment paves the way for future investigations of interaction and coherence-induced correlation effects in quantum transport.

A real-time PCR for the detection and characterisation of Aspergillus species

An early diagnosis of an invasive fungal infection is essential for the initiation of a specific antifungal therapy and to avoid unnecessary discontinuation of a baseline therapy for haematological or oncological diseases. A real-time PCR assay for the detection and strain identification of Aspergillus species from culture strains was evaluated. DNA preparation was evaluated in contaminated culture media, urine and serum. A LightCycler PCR to differentiate various Aspergillus species was established. A real-time PCR assay for the detection of Aspergillus species was improved and was able to detect and differentiate medically important Aspergillus spp. The sensitivity of the test was <10 plasmid equivalents/assay. The real-time PCR assay is a useful tool for the rapid identification of Aspergillus species and might be useful as an early diagnostic tool to detect an invasive fungal infection. A real-time PCR protocol was improved by generating plasmid standards, additional generation of melting curves for species identification and the correlation between the melting temperature and the nucleotide exchanges within the used 18S rRNA gene region.

Characterization of murine non-adherent bone marrow cells leading to recovery of endogenous hematopoiesis

Non-adherent bone marrow-derived cells (NA-BMCs) are a mixed cell population that can give rise to multiple mesenchymal phenotypes and that facilitates hematopoietic recovery. We characterized NA-BMCs by flow cytometry, fibroblast colony-forming units (CFU-f), real-time PCR, and in in vivo experiments. In comparison to adherent cells, NA-BMCs expressed high levels of CD11b(+) and CD90(+) within the CD45(+) cell fraction. CFU-f were significantly declining over the cultivation period, but NA-BMCs were still able to form CFU-f after 5 days. Gene expression analysis of allogeneic NA-BMCs compared to bone marrow (BM) indicates that NA-BMCs contain stromal, mesenchymal, endothelial cells and monocytes, but less osteoid, lymphoid, and erythroid cells, and hematopoietic stem cells. Histopathological data and analysis of weight showed an excellent recovery and organ repair of lethally irradiated mice after NA-BMC transplantation with a normal composition of the BM.

Effects of latex avoidance on latex sensitization, atopy and allergic diseases in patients with spina bifida

BACKGROUND

Ten years ago, avoidance measures such as the performance of latex-free operations were implemented in children with spina bifida. Since then, latex sensitization and latex allergy have decreased in this high-risk group.

OBJECTIVE

To study the effect of primary latex-free prophylaxis on the prevalence of allergic diseases and atopy as a marker for sensitization spreading in children with spina bifida.

METHODS

One hundred and twenty children with spina bifida born after the introduction of latex-free prophylaxis and operated on under latex-free conditions ('current group') were examined for latex sensitization, latex allergy, sensitization to aero- and food allergens and allergic diseases. Results were compared to a 'historic' (not latex-free operated) group of children with spina bifida and comparable age (n = 87) and to a recent sample of children from the general population (n = 12,403).

RESULTS

In comparison with the 'historic group', latex sensitization (55% vs 5%, P < 0.001) and latex allergy (37% vs 0.8%, P < 0.001) were significantly reduced in the 'current group'. Furthermore, a significant reduction could be demonstrated for sensitization to aeroallergens (41.4% vs 20.8%, P = 0.001) and for allergic diseases (35% vs 15%, P = 0.001). The prevalence for atopy, sensitization to aero-/foodallergens and for allergic diseases in children of the 'current group' was similar to those in children of the weighted population sample.

CONCLUSIONS

Latex avoidance in children with spina bifida prevents latex sensitization and latex allergy. Additionally, it also seems to prevent sensitization to other allergens and allergic diseases which might be explained by the prevention of sensitization spreading.

A real-time PCR assay for the differentiation of Candida species

AIMS

We established a real-time PCR assay for the detection and strain identification of Candida species and demonstrated the ability to differentiate between Candida albicans the most common species, and also Candida parapsilosis, Candida glabrata, Candida tropicalis and Candida dubliniensis by LightCycler PCR and melting curve analysis.

METHODS AND RESULTS

The DNA isolation from cultures and serum was established using the QIAmp Tissue Kit. The sensitivity of the assay was ≥ 2 genome equivalents/assay. It was possible to differentiate all investigated Candida species by melting curve analysis, and no cross-reaction to human DNA or Aspergillus species could be observed.

CONCLUSIONS

The established real-time PCR assay is a useful tool for the rapid identification of Candida species and a base technology for more complex PCR assays.

SIGNIFICANCE AND IMPACT OF THE STUDY

We carried out initial steps in validation of a PCR assay for the detection and differentiation of medically relevant Candida species. The PCR was improved by generating PCR standards, additional generation of melting curves for species identification and the possibility to investigate different specimens simultaneously.

Natural selection hampers divergence of reproductive traits in a seed beetle

Speciation is thought to often result from indirect selection for reproductive isolation. This will occur when reproductive traits that cause reproductive isolation evolve (i) as a by-product of natural selection on traits with which they are genetically correlated or (ii) as an indirect result of diversifying sexual selection. Here, we use experimental evolution to study the degree of divergent evolution of reproductive traits by manipulating the intensity of natural and sexual selection in replicated selection lines of seed beetles. Following 40 generations of selection, we assayed the degree of divergent evolution of reproductive traits between replicate selection lines experiencing the same selection regime. The evolution of reproductive traits was significantly divergent across selection lines within treatments. The evolution of reproductive traits was both slower and, more importantly, significantly less divergent among lines experiencing stronger directional natural selection. This suggests that reproductive traits did not evolve as an indirect by-product of adaptation. We discuss several ways in which natural selection may hamper divergent evolution among allopatric populations.

Female nutritional status determines the magnitude and sign of responses to a male ejaculate signal in Drosophila melanogaster

Ejaculate chemicals transferred from males to females during mating cause significant changes in female behaviour and physiology, but the causes of phenotypic variation in these responses is little understood. We tested here the effect of adult female nutrition on the response of female Drosophila melanogaster to a specific ejaculate component, the sex peptide (SP), which is of interest because of its effects on female egg laying, sexual receptivity, feeding rate, immune responses and potential role in mediating sexual conflict. We exposed adult females to five different diets and kept them continuously with males that did or did not transfer SP. Diet altered the presence, magnitude and sign of the effects of SP on different phenotypic traits (egg laying, receptivity and lifespan) and different traits responded in different ways. This showed that the set of responses to mating can be uncoupled and can vary independently in different environments. Importantly, diet also significantly affected whether exposure to SP transferring males was beneficial or costly to females, with beneficial effects occurring more often than expected. Hence, the food environment can also shape significantly the strength and direction of selection on mating responses.

Universal oscillations in counting statistics

Noise is a result of stochastic processes that originate from quantum or classical sources. Higher-order cumulants of the probability distribution underlying the stochastic events are believed to contain details that characterize the correlations within a given noise source and its interaction with the environment, but they are often difficult to measure. Here we report measurements of the transient cumulants n(m) of the number n of passed charges to very high orders (up to m = 15) for electron transport through a quantum dot. For large m, the cumulants display striking oscillations as functions of measurement time with magnitudes that grow factorially with m. Using mathematical properties of high-order derivatives in the complex plane we show that the oscillations of the cumulants in fact constitute a universal phenomenon, appearing as functions of almost any parameter, including time in the transient regime. These ubiquitous oscillations and the factorial growth are system-independent and our theory provides a unified interpretation of previous theoretical studies of high-order cumulants as well as our new experimental data.

The benefits of male ejaculate sex peptide transfer in Drosophila melanogaster

The accessory gland protein (Acp) ejaculate molecules of male Drosophila melanogaster mediate sexual selection and sexual conflict at the molecular level. However, to date no studies have comprehensively measured the timing and magnitude of fitness benefits to males of transferring specific Acps. This is an important omission because without this information it is not possible to fully understand the strength and form of selection acting on adaptations such as Acps. Here, we measured the fitness benefits to males of ejaculate sex peptide (SP) transfer. SP is of interest because it is a candidate for mediating sexual conflict: its frequent receipt reduces female fitness. In single matings with virgin females SP is known to increase egg laying and decrease receptivity. Hence, we predicted that SP could: (i) boost a male's absolute paternity by increasing offspring production and delaying female remating and/or (ii) boost relative paternity share. We tested these predictions using two different lines of SP-lacking males, in both two-mating and free-mating assay conditions. SP transfer conferred higher absolute, but not relative, male reproductive success. In matings with virgin females, SP transfer increased mating productivity and delayed remating and hence the onset of sperm competition. In already mated females, SP transfer did not elevate absolute progeny production, but did increase intermating intervals and hence the period over which a male could gain paternity. Consistent with this, under free-mating conditions over an extended period, we detected a 'per-mating' fitness benefit for males transferring SP. These benefits are consistent with a role for SP in mediating conflict, with SP acting to maximize short-term fitness benefits for males.

Physical and biological performance of a novel block copolymer nerve guide

Although the ability to regenerate is evident in the nervous system, lesioned neurites are unable to cross gaps in neuronal pathways. In order to bridge gaps, guiding cues are essential to direct neurite regrowth. To overcome many of the shortcomings of polymer-based nerve guides, we developed a bioresorbable nerve guide composed of a novel trimethylene carbonate-caprolacton block copolymer (TMC-CL). Pore formation was controlled by using special solvent/precipitation media compositions in combination with the pore forming agent poly ethylene glycol (PEG). NMR spectroscopy, shear force-, compression-, and permeation assays were used for conduit characterization. The polymer conduit has a semipermeable wall with submicron pores to allow free metabolite/drug exchange. In order to investigate the principle of temporally controlled expression of therapeutic proteins in nerve guides, Neuro-2a cells were genetically engineered to express the reporter gene product green fluorescent protein (GFP) under the control of the Tet-On system. When these transduced cells were encapsulated in nerve guides, GFP expression could be induced for days by adding the antibiotic tetracycline derivative doxycycline to the nerve guide environment. Furthermore, encapsulated dorsal root ganglia (DRG) produced long neurites in vitro. In subsequent in vivo experiments, nerve guides filled with Schwann cells (SC) were implanted into lesioned spinal cords of adult rats. Regeneration of spinal cord axons into nerve guides was promoted by co-implanted Schwann cells. The data suggest that the novel TMC-CL nerve guides provide a promising tool for neuroregeneration.

Divergence in replicated phylogenies: the evolution of partial post-mating prezygotic isolation in bean weevils

By tradition, speciation research has been focused on processes leading to either premating or post-zygotic reproductive isolation. The processes which generate isolation after mating but before zygote formation are less well understood. Here, we study divergence in characters which contribute to post-mating prezygotic isolation, such as egg production and remating rate. We propose that 'replicated' laboratory phylogenies with known histories can be used to yield insights into the processes of divergence. We performed a series of cross-matings between populations within two strains of the bean weevil Callosobruchus maculatus. Each strain has a unique and independent origin and both have been kept in the same set of laboratories during the last few decades. Our results show that divergence has occurred between laboratory populations within strains with regards to the effects that mating has on female reproductive behaviour, showing that the evolution of partial post-mating prezygotic isolation can be rapid. More importantly, the pattern of divergence across populations was distinct in the two strains, suggesting that coevolutionary trajectories are not determined by environmental factors but are to some extent arbitrary. We discuss the limitations of the novel empirical strategy employed here, and conclude that our results lend support to the hypothesis that post-mating sexual selection is capable of rapidly generating post-mating prezygotic isolation.

astray, a zebrafish roundabout homolog required for retinal axon guidance

As growing retinotectal axons navigate from the eye to the tectum, they sense guidance molecules distributed along the optic pathway. Mutations in the zebrafish astray gene severely disrupt retinal axon guidance, causing anterior-posterior pathfinding defects, excessive midline crossing, and defasciculation of the retinal projection. Eye transplantation experiments show that astray function is required in the eye. We identify astray as zebrafish robo2, a member of the Roundabout family of axon guidance receptors. Retinal ganglion cells express robo2 as they extend axons. Thus, robo2 is required for multiple axon guidance decisions during establishment of the vertebrate visual projection.

Virtual placement of frontal ventricular catheters using frameless neuronavigation: an "unbloody training" for young neurosurgeons

OBJECTIVE

To evaluate virtually the reliability of freehand puncture of the anterior horn of the lateral ventricle and to provide realistic, but unbloody training for young neurosurgeons.

METHODS

Virtual placement of ventricular catheters was performed repeatedly by neurosurgical doctors and thereafter controlled by neuronavigation. With the help of a frameless stereotactic navigation device they virtually had to hit the anterior horn of the lateral ventricle on the MRI of 29 brains with normal ventricular sizes and 60 pathological ventricles, respectively. The catheter placement was simulated using the pointer of the navigation system (EasyGuide Neuro). The monitor screen was blinded, so that on-line control was impossible. Virtual elongation of the pointer tip was performed on the workstation and the position of the virtual catheter was evaluated on a printout.

RESULTS

Virtual freehand catheter placement was performed 145 times into the MRIs of the normal brains. In 66 cases (45%) the site of the catheter tip was judged as accurate as shown by the navigation system. No difference concerning the number of correctly placed catheters was observed when comparing more and less experienced doctors. The results in the 60 pathological MRIs of patients differed with respect to the size of the ventricles: in narrow ventricles an accurate placement succeeded in 7 of 22 cases (32%), moderately enlarged ventricles were accurately hit in 15 out of 32 cases (46%) and wide ventricles in 5 of 6 attempts (83%), respectively.

CONCLUSION

This setup is a simple, practicable tool for neurosurgical education. The virtual freehand placement of ventricular drains controlled by neuronavigation provides an unbloody training of a routine neurosurgical procedure in a realistic setting without the risk of injuring a patient. Neuronavigation systems can serve therefore as a link between learning from observation and handling the real situation.

A radiation hybrid map of the zebrafish genome

Recent large-scale mutagenesis screens have made the zebrafish the first vertebrate organism to allow a forward genetic approach to the discovery of developmental control genes. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map to match them with mapped candidate genes and expressed sequence tags (ESTs). To facilitate the mapping of candidate genes and to increase the density of markers available for positional cloning, we have created a radiation hybrid (RH) map of the zebrafish genome. This technique is based on somatic cell hybrid lines produced by fusion of lethally irradiated cells of the species of interest with a rodent cell line. Random fragments of the donor chromosomes are integrated into recipient chromosomes or retained as separate minichromosomes. The radiation-induced breakpoints can be used for mapping in a manner analogous to genetic mapping, but at higher resolution and without a need for polymorphism. Genome-wide maps exist for the human, based on three RH panels of different resolutions, as well as for the dog, rat and mouse. For our map of the zebrafish genome, we used an existing RH panel and 1,451 sequence tagged site (STS) markers, including SSLPs, cloned candidate genes and ESTs. Of these, 1,275 (87.9%) have significant linkage to at least one other marker. The fraction of ESTs with significant linkage, which can be used as an estimate of map coverage, is 81.9%. We found the average marker retention frequency to be 18.4%. One cR3000 is equivalent to 61 kb, resulting in a potential resolution of approximately 350 kb.

Sesquiterpenes from lippia integrifolia essential Oil

Four sesquiterpenes (1-4) with the africanane skeleton [of which only 5-africanene (1) has been previously reported] and the new asteriscane derivative asterisca-3(15),6-diene (5) were isolated from the essential oil of Lippia integrifolia. A further new compound, african-2(6)-ene (7), was obtained as a semisynthetic product by derivatization of isoafricanol (6). The structures of the new compounds were assigned on the basis of spectroscopic data, enantioselective gas chromatography, and by chemical correlations.

Sonic hedgehog is not required for the induction of medial floor plate cells in the zebrafish

Sonic hedgehog (Shh) is a secreted protein that is involved in the organization and patterning of several tissues in vertebrates. We show that the zebrafish sonic-you (syu) gene, a member of a group of five genes required for somite patterning, is encoding Shh. Embryos mutant for a deletion of syu display defects in patterning of the somites, the lateral floor plate cells, the pectoral fins, the axons of motorneurons and the retinal ganglion cells. In contrast to mouse embryos lacking Shh activity, syu mutant embryos do form medial floor plate cells and motorneurons. Since ectopic overexpression of shh in zebrafish embryos does not induce ectopic medial floor plate cells, we conclude that shh is neither required nor sufficient to induce this cell type in the zebrafish.

Zebrafish nodal-related genes are implicated in axial patterning and establishing left-right asymmetry

Nodal-related 1 (ndr1) and nodal-related 2 (ndr2) genes in zebrafish encode members of the nodal subgroup of the transforming growth factor-beta superfamily. We report the expression patterns and functional characteristics of these factors, implicating them in the establishment of dorsal-ventral polarity and left-right asymmetry. Ndr1 is expressed maternally, and ndr1 and ndr2 are expressed during blastula stage in the blastoderm margin. During gastrulation, ndr expression subdivides the shield into two domains: a small group of noninvoluting cells, the dorsal forerunner cells, express ndr1, while ndr2 RNA is found in the hypoblast layer of the shield and later in notochord, prechordal plate, and overlying anterior neurectoderm. During somitogenesis, ndr2 is expressed asymmetrically in the lateral plate as are nodal-related genes of other organisms, and in a small domain in the left diencephalon, providing the first observation of asymmetric gene expression in the embryonic forebrain. RNA injections into Xenopus animal caps showed that Ndr1 acts as a mesoderm inducer, whereas Ndr2 is an efficient neural but very inefficient mesoderm inducer. We suggest that Ndr1 has a role in mesoderm induction, while Ndr2 is involved in subsequent specification and patterning of the nervous system and establishment of laterality.

Long-term angiographic and histopathologic findings in experimental aneurysms of the carotid bifurcation embolized with platinum and tungsten coils

PURPOSE

To evaluate the long-term outcome of endovascular occlusion of arterial aneurysms effected with metal coils.

METHODS

Microsurgical methods were used to produce carotid bifurcation aneurysms in 20 rabbits and the radiologic and histologic changes were examined. Eight of these aneurysms were occluded with electrically detachable platinum coils (Guglielmi detachable coils [GDCs] and nine were treated with mechanically detachable tungsten coils (mechanical detachable system [MDS]). Three aneurysms remained untreated and served as controls. One animal died of embolic complications 12 hours after endovascular treatment. After observation periods of 3 to 6 months, the remaining animals were examined by intraarterial digital subtraction angiography and subsequent fixation and light and electron microscopy.

RESULTS

Large open spaces without signs of thrombosis were found between the loops of the coil baskets in 12 aneurysms (six treated with GDCs and six treated with MDS) regardless of the observation period. In very densely packed aneurysms (four cases with complete occlusion as determined by angiographic criteria), the coil surfaces were for the most part covered by thin cell layers; however, complete endothelialization was never seen. In aneurysms with an initial partial occlusion of 70% to 90%, coil compaction and/or recanalization was a consistent finding. A comparison of the radiologic findings with the histologic aspect revealed that the degree of occlusion was often overrated on the radiographs (in eight of 17 cases). In general, the fibrous tissue reaction appeared to be slightly more pronounced in aneurysms occluded with tungsten coils.

CONCLUSIONS

Platinum and tungsten coils were not always effective in causing endoluminal thrombosis leading to long-term occlusion by organized thrombus.

[Endovascular treatment of cerebral aneurysms with selectively detachable platinum coils]

In 14 patients (eight men, six women; mean age 58 [31-72] years) with intracranial aneurysm (basilar artery in nine, anterior branches in five) the aneurysm was occluded by electrically detachable platinum coils, advanced into the aneurysm introduced via a percutaneously introduced catheter system, under local anaesthesia and fluoroscopic control. Ten patients had acute subarachnoid haemorrhage (stage II-IV). In two patients several sessions were required before complete occlusion was achieved. In one patient, with a basilar artery aneurysm, the aneurysmal wall was perforated (angiographically demonstrated contrast-medium extravasation), but this remained clinically asymptomatic. There has been no recurrence or renewed bleeding during a follow-up period of 6-12 months. The method is a highly promising addition to the micro-neurosurgical treatment of such aneurysms. However, as long-term results are still awaited, indications for using the method should be strict and only those patients should be so treated in whom operation would be associated with a high risk or who are inoperable.