Computational modeling of signal transduction networks kinetic parameters - Petri net approaches

More and more computational techniques have been applied to model biological systems, especially signaling pathways in medical systems. Due to the large number of experimental data driven by high-throughput technologies, new computational concepts have been developed. Nevertheless, often the necessary kinetic data cannot be determined in sufficient number and quality because of experimental complexity or ethical reasons. At the same time, the number of qualitative data drastically increased, for example, gene expression data, protein-protein interaction data, and imaging data. Especially for large-scale models, the application of kinetic modeling techniques can fail. On the other hand, many large-scale models have been constructed applying qualitative and semi-quantitative techniques, for example, logical models or Petri net models. These techniques make it possible to explore system's dynamics without knowing kinetic parameters. Here, we summarize the work of the last ten years for modeling signal transduction pathways in medical applications applying Petri net formalism. We focus on analysis techniques based on system's invariants without any kinetic parameters and show predictions of all signaling pathways of the system. We start with an intuitive introduction into Petri nets and system's invariants. We illustrate the main concepts using the TNFR1-induced NF-kB pathway as case study. Summarizing recent models, we discuss advantages and challenges of Petri net applications to medical signaling systems. Additionally, we provide exemplarily interesting Petri net applications to model signaling in medical systems of the last years that use the well-known stochastic and kinetic concepts developed about 50 years ago.

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

BACKGROUND

Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke.

RESULTS

In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected.

CONCLUSIONS

To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.

Characterisation of barley landraces from Syria and Jordan for resistance to rhynchosporium and identification of diagnostic markers for Rrs1Rh4

Diagnostic markers for Rrs1_Rh4 have been identified by testing for associations between SNPs within the Rrs1 interval in 150 barley genotypes and their resistance to Rhynchosporium commune isolates recognised by lines containing Rrs1. Rhynchosporium or barley scald, caused by the destructive fungal pathogen Rhynchosporium commune, is one of the most economically important diseases of barley in the world. Barley landraces from Syria and Jordan demonstrated high resistance to rhynchosporium in the field. Genotyping of a wide range of barley cultivars and landraces, including known sources of different Rrs1 genes/alleles, across the Rrs1 interval, followed by association analysis of this genotypic data with resistance phenotypes to R. commune isolates recognised by Rrs1, allowed the identification of diagnostic markers for Rrs1_Rh4. These markers are specific to Rrs1_Rh4 and do not detect other Rrs1 genes/alleles. The Rrs1_Rh4 diagnostic markers represent a resource that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars. Thirteen out of the 55 most resistant Syrian and Jordanian landraces were shown to contain markers specific to Rrs1_Rh4. One of these lines came from Jordan, with the remaining 12 lines from different locations in Syria. One of the Syrian landraces containing Rrs1_Rh4 was also shown to have Rrs2. The remaining landraces that performed well against rhynchosporium in the field are likely to contain other resistance genes and represent an important novel resource yet to be exploited by European breeders.

Characterisation of barley resistance to rhynchosporium on chromosome 6HS

Major resistance gene to rhynchosporium, Rrs18, maps close to the telomere on the short arm of chromosome 6H in barley. Rhynchosporium or barley scald caused by a fungal pathogen Rhynchosporium commune is one of the most destructive and economically important diseases of barley in the world. Testing of Steptoe × Morex and CIho 3515 × Alexis doubled haploid populations has revealed a large effect QTL for resistance to R. commune close to the telomere on the short arm of chromosome 6H, present in both populations. Mapping markers flanking the QTL from both populations onto the 2017 Morex genome assembly revealed a rhynchosporium resistance locus independent of Rrs13 that we named Rrs18. The causal gene was fine mapped to an interval of 660 Kb using Steptoe × Morex backcross 1 S₂ and S₃ lines with molecular markers developed from Steptoe exome capture variant calling. Sequencing RNA from CIho 3515 and Alexis revealed that only 4 genes within the Rrs18 interval were transcribed in leaf tissue with a serine/threonine protein kinase being the most likely candidate for Rrs18.

Resistance to Rhynchosporium commune in a collection of European spring barley germplasm

Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1. Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars.

Discovery of τ Neutrino Appearance in the CNGS Neutrino Beam with the OPERA Experiment

The OPERA experiment was designed to search for ν_{μ}→ν_{τ} oscillations in appearance mode, i.e., by detecting the τ leptons produced in charged current ν_{τ} interactions. The experiment took data from 2008 to 2012 in the CERN Neutrinos to Gran Sasso beam. The observation of the ν_{μ}→ν_{τ} appearance, achieved with four candidate events in a subsample of the data, was previously reported. In this Letter, a fifth ν_{τ} candidate event, found in an enlarged data sample, is described. Together with a further reduction of the expected background, the candidate events detected so far allow us to assess the discovery of ν_{μ}→ν_{τ} oscillations in appearance mode with a significance larger than 5σ.

Selective unilateral spinal anaesthesia for outpatient knee arthroscopy using real-time monitoring of lower limb sympathetic tone

Selective unilateral spinal anaesthesia is a useful approach for ambulatory lower limb surgery because it allows more rapid home discharge compared to bilateral block. Infrequent use is due to the fact that obtaining selective unilateral block can be difficult, requiring attention to technique. We present a method with a high success rate that uses real-time monitoring of the sympathetic activity of the legs. In this prospective study, 56 patients scheduled for ambulatory knee arthroscopy had spinal anaesthesia in the lateral recumbent position, with hyperbaric bupivacaine 0.5% injected at 0.33 ml/min up to a maximum dose of 5 mg. Sympathetic tone of the legs was monitored by plantar electrical dermal resistance. The clinical effect was assessed by loss of sensation and muscle strength. The haemodynamic course and adverse events were monitored. The motor block was strictly unilateral in 55 patients (98%) and the sensory block was strictly unilateral in 53 patients (94%). The median decrease in systolic blood pressure was 6 mmHg. The time from subarachnoid puncture to arrival in the recovery room was 73±23 minutes; the duration of stay in the recovery room was 70±30 minutes. Three patients with a well-established block of adequate extent required conversion to general anaesthesia because of tourniquet pain. Urinary retention only occurred in the sole patient with bilateral block. This method of performing selective unilateral spinal anaesthesia using real-time monitoring of sympathetic tone of the legs has a high success rate and is associated with rapid eligibility for home discharge.

One-dimensional weak antilocalization due to the berry phase in HgTe wires

We study the weak antilocalization (WAL) effect in the magnetoresistance of narrow HgTe wires fabricated in quantum wells with normal and inverted band ordering. Measurements at different gate voltages indicate that the WAL is only weakly affected by Rashba spin-orbit splitting and persists when the Rashba splitting is about zero. The WAL amplitude in wires with normal band ordering is an order of magnitude smaller than for wires with an inverted band structure. These observations are attributed to the Dirac-like dispersion of the energy bands in HgTe quantum wells. From the magnetic-field and temperature dependencies we extract the dephasing lengths and band Berry phases. The weaker WAL for samples with a normal band structure can be explained by a nonuniversal Berry phase which always exceeds π, the characteristic value for gapless Dirac fermions.

Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

In two Spanish barley landraces with outstanding resistance to scald, the Rrs1 Rh4 locus was fine mapped including all known markers used in previous studies and closely linked markers were developed. Scald, caused by Rhynchosporium commune, is one of the most prevalent barley diseases worldwide. A search for new resistance sources revealed that Spanish landrace-derived lines SBCC145 and SBCC154 showed outstanding resistance to scald. They were crossed to susceptible cultivar Beatrix to create large DH-mapping populations of 522 and 416 DH lines that were scored for disease resistance in the greenhouse using two R. commune isolates. To ascertain the pattern of resistance, parents and reference barley lines with known scald resistance were phenotyped with a panel of differential R. commune isolates. Subpopulations were genotyped with the Illumina GoldenGate 1,536 SNP Assay and a large QTL in the centromeric region of chromosome 3H, known to harbour several scald resistance genes and/or alleles, was found in both populations. Five SNP markers closest to the QTL were converted into CAPS markers. These CAPS markers, together with informative SSR markers used in other scald studies, confirmed the presence of the Rrs1 locus. The panel of differential scald isolates indicated that the allele carried by both donors was Rrs1 Rh4 . The genetic distance between Rrs1 and its flanking markers was 1.2 cM (11_0010) proximally and 0.9 cM (11_0823) distally, which corresponds to a distance of just below 9 Mbp. The number and nature of scald resistance genes on chromosome 3H are discussed. The effective Rrs1 allele found and the closely linked markers developed are already useful tools for molecular breeding programs and provide a good step towards the identification of candidate genes.

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

The transition from vegetative growth to reproductive development is a complex process that requires an integrated response to multiple environmental cues and endogenous signals. In Arabidopsis thaliana, which has a facultative requirement for vernalization and long days, the genes of the autonomous pathway function as floral promoters by repressing the central repressor and vernalization-regulatory gene FLC. Environmental regulation by seasonal changes in daylength is under control of the photoperiod pathway and its key gene CO. The root and leaf crop species Beta vulgaris in the caryophyllid clade of core eudicots, which is only very distantly related to Arabidopsis, is an obligate long-day plant and includes forms with or without vernalization requirement. FLC and CO homologues with related functions in beet have been identified, but the presence of autonomous pathway genes which function in parallel to the vernalization and photoperiod pathways has not yet been reported. Here, this begins to be addressed by the identification and genetic mapping of full-length homologues of the RNA-regulatory gene FLK and the chromatin-regulatory genes FVE, LD, and LDL1. When overexpressed in A. thaliana, BvFLK accelerates bolting in the Col-0 background and fully complements the late-bolting phenotype of an flk mutant through repression of FLC. In contrast, complementation analysis of BvFVE1 and the presence of a putative paralogue in beet suggest evolutionary divergence of FVE homologues. It is further shown that BvFVE1, unlike FVE in Arabidopsis, is under circadian clock control. Together, the data provide first evidence for evolutionary conservation of components of the autonomous pathway in B. vulgaris, while also suggesting divergence or subfunctionalization of one gene. The results are likely to be of broader relevance because B. vulgaris expands the spectrum of evolutionarily diverse species which are subject to differential developmental and/or environmental regulation of floral transition.

Backscattering of Dirac fermions in HgTe quantum wells with a finite gap

The density-dependent mobility of n-type HgTe quantum wells with inverted band ordering has been studied both experimentally and theoretically. While semiconductor heterostructures with a parabolic dispersion exhibit an increase in mobility with carrier density, high-quality HgTe quantum wells exhibit a distinct mobility maximum. We show that this mobility anomaly is due to backscattering of Dirac fermions from random fluctuations of the band gap (Dirac mass). Our findings open new avenues for the study of Dirac fermion transport with finite and random mass, which so far has been hard to access.

A survey of EMS-induced biennial Beta vulgaris mutants reveals a novel bolting locus which is unlinked to the bolting gene B

Beta vulgaris is a facultative perennial species which exhibits large intraspecific variation in vernalization requirement and includes cultivated biennial forms such as the sugar beet. Vernalization requirement is under the genetic control of the bolting locus B on chromosome II. Previously, ethyl methanesulfonate (EMS) mutagenesis of an annual accession had yielded several mutants which require vernalization to bolt and behave as biennials. Here, five F2 populations derived from crosses between biennial mutants and annual beets were tested for co-segregation of bolting phenotypes with genotypic markers located at the B locus. One mutant appears to be mutated at the B locus, suggesting that an EMS-induced mutation of B can be sufficient to abolish annual bolting. Co-segregation analysis in four populations indicates that the genetic control of bolting also involves previously unknown major loci not linked to B, one of which also affects bolting time and was genetically mapped to chromosome IX.

Continuous biogas production from fodder beet silage as sole substrate

Since April 2000 a two-step anaerobic plant with two subsequent 500 m3 reactors has been producing biogas from fodder beet silage (pH 3.4-4.1) as the sole substrate. The plant is located at Kirchlengern near Bielefeld, Germany. Initially the reactors were inoculated with swine manure at 37 degrees C. After a start-up phase the process was sustained at pH 7.5-8.0 by feeding the silage as sole substrate with an HRT of about 55 d twice a day. Parallel to the biogas plant at Kirchlengern four one-step laboratory reactors were continuously driven at temperatures of 37 degrees C, 45 degrees C, 60 degrees C and 65 degrees C. They were fed with the same silage, but only once per day (one impulse). The organic loading rate (OLR) was adjusted to 3.9 g volatile solids (VS)/(l*d) with a concomitant hydraulic retention time (HRT) of 27 d. There was no problem with starting the reactors, but after 86 days the volumetric gas production of the 65 degrees C reactor ceased and a high amount of approximately 65 mM propionate could be determined. By decreasing the temperature down to 60 degrees C a stable reactor performance was recovered for a period of at least 600 further days. Interestingly microscopic analyses revealed that the morphology of methanogenic bacteria in the 60 degrees C was quite different from the 37 and 45 degrees C reactor exhibiting only rodlike methanogens whereas at 37 degrees C coccoid morphotypes besides rodlike methanogens were dominant. In a 55 degrees C reactor (separate experiment) a mixture of coccoid and rodlike methanogens established. During impulse feeding with 3.9 g (VS)/(l*d) it was observed that the quickest recovery of gas production, the pH, CH4 and CO2 content as well as the redox value could be observed at 37 degrees C or at 45 degrees C. Recovery of 75% gas volume (related to the value before or after impulse feeding) was obtained after 5.5 and 7.5 h of feeding time point whereas the 60 degrees C reactor needed 16 h. Slight significant differences were seen in the spectrum of volatile fatty acids (VFA) reaching at 37 degrees or 45 degrees C its maximum with 10-30 mM total VFA at 2-3 h after feeding. After this the VFA level declined to nearly zero (except for the 60 degrees C reactor). Therefore the 37 degrees C reactor was favoured. A double experiment with a second 37 degrees C reactor was started by a somewhat different inoculation procedure from the remaining 3 reactors, but revealed similar results. An impulse feeding experiment with a very high OLR of 16.5 g (VS)/(l*d) lasting 1 week offered a stable reactor performance with a peak GPR of up to 24 l/(l reactor *d) and an HRT of 5.45d. Therefore a long term operation with an HRT of only 7.5 days and an OLR of 12 g (VS)/(l*d) should be possible. By increasing the temperature no significantly different specific gas production rates and methane yields could be observed, e.g. it gave 600-7001 biogas from 1 kg VS. The corresponding methane content ranged between 62-64%. With a methane content of 63 +/- 1% a yield of 40.1 +/- 2 m3 methane/ton fresh fodder beet silage was obtained.

Development and characterization of a tamoxifen-resistant breast carcinoma xenograft

A human tamoxifen-resistant mammary carcinoma, MaCa 3366/TAM, originating from a sensitive parental xenograft 3366 was successfully established by treatment of tumour-bearing nude mice with 1-50 mg kg(-1) tamoxifen for 3 years during routine passaging. Both tumours did not differ significantly in OR- and PR-positivity, however, when compared with the sensitive tumour line, the mean OR content of the TAM-resistant subline is slightly lower. An OR-upregulation following withdrawal of oestradiol treatment was observed in the parental tumours but not in the resistant xenografts. Following long-term treatment with tamoxifen, the histological pattern of the breast carcinoma changed. The more differentiated structures being apparent after treatment with 17beta-oestradiol in the original 3366 tumour were not induced in the resistant line. Tamoxifen failed to induce a tumour growth inhibition in comparison to the tamoxifen-sensitive line. The pure anti-oestrogen, ICI 182 780, revealed cross-resistance. Sequence analysis of the hormone-binding domain of the OR of both lines showed no differences, suggesting that either mutations in other regions of the OR are involved in the TAM-resistance phenotype or that mechanisms outside of this protein induced this phenotype. Oestrogen and anti-oestrogen regulate pS2 and cathepsin D expression in 3366 tumours as in the human breast cancer cell line MCF-7. The resistant 3366/TAM tumours have lost this regulation. The established breast cancer xenografts 3366 and 3366/TAM offer the possibility of investigating mechanisms of anti-oestrogen resistance in an in vivo situation. They can be used to test novel approaches to prevent, or to overcome, this resistance in a clinically related manner.

Relation of oestradiol-mediated growth stimulation with the expression of c-erbB-2 protein in xenotransplanted oestradiol-receptor-positive and -negative breast carcinomas

Attempts were made to correlate growth effects induced by oestradiol and tamoxifen with the hormonal regulation of c-erbB-2 protein in experiments in vivo. We report here the responsiveness of four xenotransplanted oestrogen-receptor(ER)-positive and four ER-negative human mammary carcinomas to oestradiol and tamoxifen. Oestradiol in a dose of 0.5 mg/kg significantly increased the growth of the ER-positive mammary carcinomas 3366, MCF-7, 4134 and 4049, but not the ER-negative tumours 4000, 4296 and MT-3. However, within the group of the ER-negative breast carcinomas the tumour 4151 ES deviates from this growth behaviour, as we could prove an estrogen induced growth. The stimulation of tumour growth by oestradiol was always accompanied by a down-regulation of c-erbB-2 protein both in the ER-positive mammary carcinomas and in the ER-negative mammary carcinoma 4151 ES. Tamoxifen significantly inhibited the growth of the ER/PR-positive mammary carcinomas 3366 and MCF-7 but not the ER-positive/PR-negative mammary carcinomas 4049 and 4134. In the group of ER-negative mammary carcinomas only the growth of the oestrogen-responsive tumour 4151 ES was significantly inhibited by tamoxifen. The inhibition of tumour growth by tamoxifen was correlated with a reversion of the oestradiol-induced down-regulation of c-erbB-2, also in the ER-negative/oestradiol-responsive mammary carcinoma 4151 ES. From our results we hypothesize that the oestrogen-dependent growth of ER-negative breast carcinoma 4151 ES could also be correlated with the oestradiol-regulated expression of c-erbB-2 protein.

Establishment and characteristics of two new human mammary carcinoma lines serially transplantable in nude mice

Two human mammary carcinomas of postmenopausal women were successfully transplanted into nude mice. Both tumours were classified as epidermal-growth-factor-, oestradiol- and progesterone-receptor-negative and c-erbB2-protein-positive. Histological studies of the primary tumours (4000 and 4151) revealed ductal invasive mammary carcinomas. In the first passages the precondition for the growth of breast carcinoma 4000 were pretreatments of the nude mice with oestradiol and peanut oil before transplantation. The mammary carcinomas 4000 and 4151 described here are suitable for in vivo testing of antineoplastic substances and for biological studies.

Characterization of two human mammary carcinomas, MT-1 and MT-3, suitable for in vivo testing of ether lipids and their derivatives

The human mammary carcinomas MT-1 and MT-3 originate from surgical material and were transplanted in nude mice. Both tumors have been classified as estradiol- and progesterone receptor-negative. Therapeutic doses of hormones and anti-hormones remained without growth inhibitory effect. MT-1 and MT-3 proved to be sensitive to conventional cytostatic drugs used for treatment of mammary carcinomas; striking is their sensitivity to ether lipids. Therefore, they are considered suitable tumor models for this class of substances.

Establishment and characterization of a new human oestradiol- and progesterone-receptor-positive mammary carcinoma serially transplantable in nude mice

A human mammary carcinoma originating from a postmenopausal patient was successfully transplanted into nude mice. According to the adopted criteria the tumour proved to be oestradiol- and progesterone-receptor-positive. Histological studies of the patient tumour revealed a ductal invasive mammary carcinoma with 80% tubular growth pattern. Following transplantation the adenoid structures decreased to 30%; the mitosis rate and grade of malignancy increased. Treatment of the nude mice with 20 micrograms oestradiol benzoate/mouse caused a loss of the oestradiol receptor of the mammary carcinoma. The mammary carcinoma 3366 can be used for testing of antineoplastic substances, antihormones and for studies in regard to down-regulation or blocking of hormone receptors and possible consequences for therapies.