A scientist's guide for submitting data to ZFIN

The Zebrafish Model Organism Database (ZFIN; zfin.org) serves as the central repository for genetic and genomic data produced using zebrafish (Danio rerio). Data in ZFIN are either manually curated from peer-reviewed publications or submitted directly to ZFIN from various data repositories. Data types currently supported include mutants, transgenic lines, DNA constructs, gene expression, phenotypes, antibodies, morpholinos, TALENs, CRISPRs, disease models, movies, and images. The rapidly changing methods of genomic science have increased the production of data that cannot readily be represented in standard journal publications. These large data sets require web-based presentation. As the central repository for zebrafish research data, it has become increasingly important for ZFIN to provide the zebrafish research community with support for their data sets and guidance on what is required to submit these data to ZFIN. Regardless of their volume, all data that are submitted for inclusion in ZFIN must include a minimum set of information that describes the data. The aim of this chapter is to identify data types that fit into the current ZFIN database and explain how to provide those data in the optimal format for integration. We identify the required and optional data elements, define jargon, and present tools and templates that can help with the acquisition and organization of data as they are being prepared for submission to ZFIN. This information will also appear in the ZFIN wiki, where it will be updated as our services evolve over time.

Histamine H4 receptor knockout mice display reduced inflammation in a chronic model of atopic dermatitis

BACKGROUND

The histamine H4 receptor (H4R) was brought into focus as a new therapeutic target for the treatment of allergic disorders such as atopic dermatitis (AD). H4R antagonists have already been tested in several animal models of AD, but these studies have yielded conflicting results.

MATERIAL AND METHODS

The development of ovalbumin-induced AD-like skin lesions was analysed in H4R(-/-) mice and in H4R antagonist (JNJ28307474)-treated mice.

RESULTS

H4R(-/-) mice showed a clear amelioration of the skin lesions, with a diminished influx of inflammatory cells and a reduced epidermal hyperproliferation at lesional skin sites. H4R(-/-) mice had a reduced amount of ovalbumin-specific IgE, a reduced number of splenocytes and lymph node cells with a decreased number of CD4+ T cells. The H4R modulated the cytokine secretion of CD4+ T cells and splenocytes and altered the cellular profile in the lymph nodes. The anti-inflammatory effect could only partially be mimicked by JNJ28307474 and only when the H4R antagonist was given during sensitization and challenge and not when JNJ28307474 was only given during the provocation phase of the allergic reaction.

CONCLUSION

The H4R modulates inflammation in a chronic allergic dermatitis setting. However, results of this study indicate that it is necessary to block the H4R during ontogeny and development of the allergic inflammation.

Effects of renal denervation on renal pelvic contractions and connexin expression in rats

AIMS

The renal pelvis shows spontaneous rhythmic contractile activity. We assessed to what extent this activity depends on renal innervation and studied the role of connexins in pelvic contractions.

METHODS

Rats underwent unilateral renal denervation or renal transplantation. Renal pelvic pressure and diuresis were measured in vivo. Spontaneous and agonist-induced contractions of isolated renal pelves were investigated by wire myography. Rat and human renal pelvic connexin mRNA abundances and connexin localization were studied by real-time PCR and immunofluorescence respectively.

RESULTS

Renal denervation or transplantation increased renal pelvic pressure in vivo by about 60 and 150%, respectively, but did not significantly affect pelvic contraction frequency. Under in vitro conditions, isolated pelvic preparations from innervated or denervated kidneys showed spontaneous contractions. Pelves from denervated kidneys showed about 50% higher contraction frequencies than pelves from innervated kidneys, whereas contraction force was similar in pelves from denervated and innervated kidneys. There was no denervation-induced supersensitivity to noradrenaline or endothelin-1. Renal denervation did not increase pelvic connexin37, 40, 43 or 45 mRNA abundances. Gap junction blockade had no effect on spontaneous pelvic contractile activity.

CONCLUSIONS

The denervation-induced effect on pelvic pressure may be the consequence of the enhanced diuresis. The mechanisms underlying the denervation-induced effects on pelvic contraction frequency remain unknown. Our data rule out a major role for two important candidates, by showing that renal denervation neither induced supersensitivity to contractile agonists nor increased connexin mRNA abundance in the pelvic wall.

Enamel surface alterations after repeated conditioning with HCl

Background

The aim of this study was to investigate the influence of etching time with 15 % hydrochloric acid (HCl) on the enamel surface destruction by studying the resulting roughness and erosion depth.

Methods

The vestibular surfaces of 12 extracted, caries free human incisors were divided into four quadrants, and each quadrant was etched with 15 % HCl for different numbers of etching cycles (1×2, 2×2, 3×2 and 4×2 min). Surface roughness and erosion depth were measured quantitatively with optical profilometry, and the surface morphology was imaged with scanning electron microscopy (SEM).

Results

After two minutes of 15 % HCl application a median enamel substance loss of 34.02 μm was observed. Lengthening of etching time (2×2, 3×2 and 4×2 min) resulted in significantly increase in erosion depth to each additionally, between 13.28 -15.16 μm (p < 0.05) ending up in a total median enamel surface loss of 77 μm. Regarding surface roughness no significant (p > 0.05) difference was found between unetched enamel and the etched enamel surfaces.

Conclusion

Repeated 15 % HCl conditioning of the enamel surface increases the depth of the etched surface erosion. However, the total erosion depth is rather shallow and therefore negligible.

[Ambulatory care of patients with asthma in Germany and disease management program for asthma from the view of statutory health insured patients. A postal survey of statutory health insured patients]

BACKGROUND

In spite of a decline in mortality due to asthma in Germany various studies point towards deficits in asthma care. Our investigation should collect data about ambulatory care from the view of statutory health insured patients (SHI), who participate in the disease management program asthma (DMP-P) or do not (NP). Primary question was, if there is a difference between asthma control. Secondary questions referred to process parameters.

METHODS

The postal inquiry was conducted in 2010 with 8000 randomly selected members of a SHI company with asthma (4000 DMP-P and 4000 NP). The descriptive evaluation of categorical items was performed with cross-tables. The absolute risk reduction (ARR) and 97.5 %-confidence interval (CI; multiple level 5 %) was used to evaluate the primary question. Secondary questions were analysed by ARR and 95 %-CI.

RESULTS

The response rate of the questionnaire accounted for 31.1 % (2565). 49.2 % of all respondents lived with an uncontrolled asthma with no differences between DMP-P and NP (ARR -2.7 %, 97.5 %-CI -7.9 -2.4 %). Results did not alter after adjustment for sex and age. The secondary questions revealed significant differences (DMP-P vs. NP) in participation in asthma trainings 50.6 vs. 32.3 %, use of a peak-flow-meter 49.3 vs. 25.3 % and asthma action plan within reach 21.7 vs. 11.0 %.

CONCLUSION

Half of all respondents lives selfreported - even in the DMP-group - with an uncontrolled asthma. Process parameters showed better results in the DMP-group. It can be considered, that the DMP has its desired effect on patient-centered care, but does not lead to a better therapeutic outcome. Explanations can only be assumed: insufficient impact of the process parameters on the outcome, patient behavior, that minimizes a possible effect, or selection effects, if patients, who were more sick and at the same time more motivated, were mainly included in the DMP. These aspects should be addressed in studies with a prospective design.

[Case control trial on putative factors antagonising the successful project course of MD thesis projects]

INTRODUCTION

Award of the degree MD has special relevance in Germany since the underlying research project can be started during the qualification for admission to doctoral training. This leads to a large number of thesis projects with a not always sufficiently pronounced enthusiasm and thus poor chances of success. Accordingly a case control study was undertaken in the Department of Human Medicine, Witten/Herdecke University to investigate reported drop-outs of thesis projects.

MATERIAL AND METHOD

In autumn 2012 all students in the clinical phases of human medicine education were surveyed using a self-conceived questionnaire on previously initiated or terminated thesis projects, "terminated" is defined as the unsuccessful ending of a project after working for at least 3 months. Individually reported thesis terminations were evaluated using defined items in a 4-stage Likert scale regarding thesis plan and project, subsequently, graduate students who successfully completed a project received the same questionnaire. The items possibly corresponding to process determinants were averaged to a total of 7 dimensions prior to the analysis; the resulting scores were normalised in value ranges 0.0 to 1.0 (1.0 = optimal project situation) whereby individual items could be included in several scores. By means of 5 items a primary endpoint from the faculty's perspective on "compliance with formal procedures" was aggregated; by means of a two-sided Wilcoxon test at the 5 % level students with unsuccessful and successful courses were compared along the corresponding scores.

RESULTS

181 of 276 students from 7 study semesters participated in the screening; details of 17 terminations and 23 currently successful courses could be evaluated in the case control study. For significant differences (p < 0.001) between unsuccessful and successful courses in the primary endpoint, median scores of 0.17 (0.07-0.50) versus 0.73 (0.53-0.83) were estimated.

CONCLUSION

There were differences between unsuccessful and (as yet) successful courses, especially with regard to the aspects "compliance with formal procedures". Thus a recommendation can be derived in the sense of a stricter and, if necessary, sanctioning demand for formal procedures such as early reporting of thesis projects to the responsible committees. A weakness is the low number of evaluable self-reported drop-outs as well as the overall moderate response rate.

[Randomised pilot study for quantification of benefit from the patient's point of view of deep oscillation treatment in primary wound healing]

BACKGROUND AND AIM OF THE INVESTIGATION: Deep oscillation refers to an electromechanical therapy method in which electrostatic attraction and friction, produced by the use of a hand-held applicator, create resonance vibrations in treated tissue. In a pilot clinical trial the impact of deep oscillation has been examined in relation to the physiological parameters of wound healing on postoperative wounds.

MATERIAL AND METHODS

Following osteosynthesis operations (extremities and spinal column), 40 patients were stratified by operation localisation and randomised into two samples (intervention [n = 20], control [n = 20]). Aside from primary care of the operation wound, finding-oriented deep oscillation was applied for at least one week following the operation in the intervention sample. The intra-individual reduction in postoperative pain occurrence between day 2 and day 7 of the postsurgical period was quantified by means of a visual analogue scale (VAS) serving as primary clinical end point from the patient's point of view. Confirmatory analysis of this primary endpoint was based on a two-sample Wilcoxon test at the 5 % level of significance.

RESULTS

According to VAS pain occurrence declined in the intervention group from day 2 to day 7 in the postoperative period by a median of 3 points (P) (quartile range -4-0.25 P) and a mean of -2.3 P, the control group remained (almost) unaltered with a median difference of 0 P (-2-0 P) and a mean difference of -0.85 P; the treatment groups differed significantly in the postoperative profile of VAS-based pain sensation (Wilcoxon p = 0.006). None of the secondary endpoints showed any locally significant sample differences.

DISCUSSION

These results demonstrate a significant pain-alleviating effect of deep oscillation. However, the exact physiological effects underpinning the impact of deep oscillation are still not completely understood.

[Language barriers in the care for pediatric immigrant patients -- results of a pilotstudy among pediatricians in Germany]

BACKGROUND

In 2010, 19.3% of German inhabitants were either first or second generation immigrants. Language barriers can potentially impair quality of care of this heterogenous group of patients. It has not yet been studied how pediatricians practicing in Germany experience and cope with language barriers.

METHODS

We conducted a written survey among participants of the 105th annual meeting of the German Society of Pediatrics in 2009. The questionnaire was newly developed and consisted of 39 items and 3 open questions. Frequency distribution and cross tables were used for descriptive analysis of categorical data.

RESULTS

229 participants returned the questionnaire (40% in inpatient care, 33% in private practice, 26% in public outpatient services). 75% of participants are confronted with language barriers regularly. The most widespread strategy to overcome barriers is using bilingual colleagues, employees or patient family members as interpreters. The opportunity to access professional interpreters depends on the care setting (22% [inpatient care] vs. 5% [private practice] vs. 28% [public outpatient service]). 91% claim that the expenditure of time to organize professional interpreting services is high.

CONCLUSION

The results of the pilot project suggest that the possibilities to overcome language barriers largely depend on the care setting. A high amount of organizational work and vague financing currently limit the use of professional interpreting services. However, health politics and science increasingly demand their use.

KIBRA gene variants are associated with episodic memory in healthy elderly

The first hypothesis free genome wide association study on cognition recently revealed the thus far unknown association of a single nucleotide polymorphism (SNP) of the KIBRA gene with episodic memory in healthy young and middle aged volunteers. Here, we report the first independent replication of this finding in an in-depth characterized sample of healthy elderly subjects. The effectsizes of the respective KIBRA SNP on memory even exceed those of the initial report. In parallel to the first study, the effect is restricted to hippocampus-related episodic memory without effects on frontal lobe function. The impact of KIBRA on memory is most likely of high relevance in elderly subjects as it is in young.

QSPR analysis of the partitioning of vaporous chemicals in a water-gas phase system and the water solubility of liquid and solid chemicals on the basis of fragment and physicochemical similarity and hybot descriptors

QSPR analyses of the solubility in water of 558 vapors, 786 liquids and 2045 solid organic neutral chemicals and drugs are presented. Simultaneous consideration of H-bond acceptor and donor factors leads to a good description of the solubility of vapors and liquids. A volume-related term was found to have an essential negative contribution to the solubility of liquids. Consideration of polarizability, H-bond acceptor and donor factors and indicators for a few functional groups, as well as the experimental solubility values of structurally nearest neighbors yielded good correlations for liquids. The application of Yalkowsky's "General Solubility Equation" to 1063 solid chemicals and drugs resulted in a correlation of experimental vs calculated log S values with only modest statistical criteria. Two approaches to derive predictive models for solubility of solid chemicals and drugs were tested. The first approach was based on the QSPR for liquids together with indicator variables for different functional groups. Furthermore, a calculation of enthalpies for intermolecular complexes in crystal lattices, based on new H-bond potentials, was carried out for the better consideration of essential solubility- decreasing effects in the solid state, as compared with the liquid state. The second approach was based on a combination of similarity considerations and traditional QSPR. Both approaches lead to high quality predictions with average absolute errors on the level of experimental log S determination.

Synthesis and structure-activity relationships of a new model of arylpiperazines. Study of the 5-HT(1a)/alpha(1)-adrenergic receptor affinity by classical hansch analysis, artificial neural networks, and computational simulation of ligand recognition

A classical quantitative structure-activity relationship (Hansch) study and artificial neural networks (ANNs) have been applied to a training set of 32 substituted phenylpiperazines with affinity for 5-HT(1A) and alpha(1)-adrenergic receptors, to evaluate the structural requirements that are responsible for 5-HT(1A)/alpha(1) selectivity. The resulting models provide a significant correlation of electronic, steric, and hydrophobic parameters with the biological affinities. Although the derived linear Hansch correlations give good statistics and acceptable predictions, the introduction of nonlinear relationships in the analysis gives more solid models and more accurate predictions. In the ANN models on the basis of the obtained 3D plots, the 5-HT(1A) affinity has a nonlinear dependence on F, V(o), V(m), and pi(o), although the nonlinear relationship is not far from a planar one. The alpha(1)-adrenergic receptor affinity has a clear nonlinear dependence on F, V(o), V(m), pi(o), and pi(m). A comparison of both analyses gives an additional understanding for 5-HT(1A)/alpha(1) selectivity: (a) high F values increase the binding affinity for 5-HT(1A) receptors and decrease the affinity for alpha(1) sites; (b) the hydrophobicity at the meta-position has only influence for the alpha(1)-adrenergic receptor; (c) the meta-position seems to be implicated in the 5-HT(1A)/alpha(1) selectivity. While the 5-HT(1A) receptor is able to accommodate bulky substituents in the region of its active site, the steric requirements of the alpha(1)-adrenergic receptor at this position are more restricted. This information was used for the design of the new ligand EF-7412 (33) (5-HT(1A): K(i exptl) = 27 nM, alpha(1): K(i exptl) > 1000 nM; 5-HT(1A): K(i pred) (ANN) = 36 nM, alpha(1): K(i pred ANN) = 2745 nM) which was characterized as an antagonist in vivo in pre- and postsynaptic 5-HT(1A)R sites. Computational simulations of the complex between EF-7412 (33) and a 3D model of the transmembrane domain of the 5-HT(1A) receptor allowed us to define the molecular details of the ligand-receptor interaction that includes: (i) the ionic interaction between the protonated amine of the ligand and Asp 3.32; (ii) the hydrogen bonds between the m-NHSO(2)Et group of the ligand and Asn 7.39; and the hydrogen bonds between the hydantoin moiety of the ligand and (iii) Thr 3.37, (iv) Ser 5.42, and (v) Thr 5.43. These QSAR and ANN results in combination with computational simulations of ligand recognition will be useful for the design of potent selective 5-HT(1A) ligands.

Substrate translocation kinetics of excitatory amino acid carrier 1 probed with laser-pulse photolysis of a new photolabile precursor of D-aspartic acid

Here we report the synthesis and photochemical and biological characterization of a new photolabile precursor of D-aspartic acid, alpha-carboxynitrobenzyl-caged D-aspartate (alpha-CNB-caged D-aspartate), and its application for studying the molecular mechanism of the neuronal excitatory amino acid carrier 1 (EAAC1). Investigation of the photochemical properties of alpha-CNB-caged D-aspartate by transient absorption spectroscopy of the aci-nitro intermediate revealed that it photolyzes with a quantum yield of 0. 19 at pH 7.0. The major component of the aci-nitro intermediate (77% of the total absorbance) decays with a time constant of 26 s. This decay is slowed by only a factor of 2 when increasing the pH to 10. A minor component (21%) decays with a time constant of 410 s and is pH insensitive. The compound was tested with respect to its biological activity with the glutamate transporter EAAC1 expressed in HEK293 cells. Whole-cell current recordings from these cells in the presence and absence of alpha-CNB-caged D-aspartate demonstrated that the compound neither activates nor inhibits EAAC1. Upon photolysis, D-aspartate-mediated whole-cell currents were generated. In contrast to laser-pulse photolysis experiments with alpha-CNB-caged L-glutamate, only a minor and much slower transient current component was observed. These results indicate that the substrate translocation step, which is not rate-limiting for the overall turnover of the transporter with L-glutamate, becomes rate-limiting when D-aspartate is translocated. The results demonstrate that the new caged D-aspartate derivative is a useful tool for the investigation of the molecular mechanism of glutamate transporters and probably other aspartate translocating systems using rapid chemical kinetic techniques.

Synthesis and photochemistry of a photolabile precursor of N-methyl-D-aspartate (NMDA) that is photolyzed in the microsecond time region and is suitable for chemical kinetic investigations of the NMDA receptor

The amino acid L-glutamate is a major neurotransmitter at excitatory synapses within the central nervous system. Neuronal responses to glutamate are mediated by at least three receptor types, one of which is the NMDA subtype, named for its specific ligand N-methyl-D-aspartic acid. Neurotransmitter receptors are transmembrane proteins that can form ion channels upon binding a specific ligand and are involved in many physiological activities of the brain and in some neurological disorders. Elucidating the mechanisms of the formation of transmembrane receptor-channels and of receptor regulation and inhibition is necessary for understanding nervous system function and for designing potential therapeutic agents. This has been hampered by the lack of rapid reaction techniques suitable for investigating protein-mediated reactions on cell surfaces. Recently a laser-pulse photolysis technique was developed to study the chemical reactions of channel-forming receptor proteins in the microsecond-to-millisecond time region. To apply the technique to NMDA1 receptors a photolabile NMDA precursor (beta-DNB NMDA) was synthesized. In this precursor the side chain carboxylate was protected as a photosensitive 2,2'-dinitrobenzhydryl ester. Photolysis with 308 nm laser light generated free NMDA with a time constant of 4.2 +/- 0.1 microseconds at pH 7 and a photolysis quantum yield of 0.18 +/- 0.05. In rat hippocampal neurons the beta-DNB NMDA (250 microM) neither activated endogenously expressed receptors nor potentiated or inhibited the NMDA response. Equilibration of hippocampal neurons in the whole-cell current recording mode with 250 microM caged precursor followed by a pulse of 333 nm laser light resulted in a rapid current rise with a rate constant of 100 s-1 due to opening of NMDA-activated receptor-channels. The caged NMDA precursor described here now makes it possible to investigate the mechanism of NMDA receptors in the micro- to millisecond time region.

Synthesis and photochemical properties of a kainate precursor and activation of kainate and AMPA receptor channels on a microsecond time scale

Kainate and alpha-amino-3-hydroxy-5-methyl-4-isoxazolylpropionate (AMPA) receptors are transmembrane proteins that can form ion channels upon binding a specific ligand. The receptors are located at major excitatory synapses in the mammalian central nervous system. Kainate and AMPA receptors participate in many physiological activities of the brain, including learning and memory, and are involved in many neurological disorders. Elucidation of the mechanisms of receptor transmembrane channel formation, inhibition, and regulation is important in understanding fundamental central nervous system function and in designing potential therapeutic agents. Kainate can activate both kainate and AMPA receptors, leading to channel opening in the microsecond to millisecond time region. A newly developed laser pulse photolysis technique, with a microsecond time resolution, has been successfully used to study the chemical reactions of receptor proteins in the microsecond to millisecond time region. To apply the technique to kainate and AMPA receptors, a photolabile kainate precursor in which a caging group, the alpha-carboxy-2-nitrobenzyl group, is attached to the gamma-carboxyl group of kainic acid has been synthesized. The photolytic release of free kainate from the caged kainate on the microsecond time scale, initiated by a pulse of laser light at 308 nm, was measured. The quantum yield is 0.34 at pH 6.8 and room temperature. The half-life of the major component (approximately 86%) of the photolytic reaction is 45 microseconds, while that of the minor component (approximately 14%) is 0.7 ms. The effects of the caged kainate on kainate and AMPA receptors endogenously expressed in rat hippocampal neurons were also evaluated. Caged kainate (750 microM) did not activate the receptor channels, nor did it potentiate or inhibit the kainate response. Photolysis of the caged kainate by a pulse of 333-nm laser light resulted in a rapid rise (with a t1/2 of 0.4 ms) in the whole-cell current due to the opening of kainate-activated receptor channels. The results presented demonstrate that this kainate precursor is suitable for rapid chemical kinetic investigations of the kainate and AMPA receptors in the microsecond to millisecond time region.

Structure of the carbohydrate moiety of human interferon-beta secreted by a recombinant Chinese hamster ovary cell line

The carbohydrate structure of the major oligosaccharide of human interferon-beta (IFN-beta) synthesized by a genetically engineered Chinese hamster ovary cell line has been determined. Analysis of the glycopeptidase F-released carbohydrates by sequential exoglycosidase treatment, methylation analysis, and fast atom bombardment-mass spectrometry revealed that 95% of the IFN-beta oligosaccharides had the following structure: (Formula: see text). The remaining 5% of the carbohydrates are probably tri- or higher antennary oligosaccharide chains. The major oligosaccharide of the recombinant IFN-beta is remarkably homogeneous with respect to terminal galactose sialylation. NeuAc, which is alpha 2-3-linked to galactose in the human IFN-beta secreted by Chinese hamster ovary cells, can be re-incorporated with an alpha 2-6 linkage in vitro, into enzymatically desialylated IFN-beta using rat liver Gal beta 1-4GlcNAc alpha 2-6 sialyltransferase. The sugar chain is important for maintaining protein solubility as shown by the fact that IFN-beta protein precipitates after deglycosylation with glycopeptidase F.