Generalisation of a procedure for computing transcription factor profiles

The limited amount of quantitative experimental data generated from life-science experiments poses a major challenge in systems biology. The reason for this is that many systems approaches, such as parameter estimation, simulation and sensitivity analysis make use of models or analyse quantitative data. However, these techniques are only of limited use if only qualitative or semi-quantitative information is available about a system. Therefore procedures that generate quantitative data from experiments in the life sciences can greatly expand the use of systems approaches to biological problems. This study addresses this issue as it introduces a procedure that computes quantitative transcription factor profiles from fluorescent microscopy data collected from green fluorescent protein (GFP) reporter cells. This technique forms a generalisation of a method that has recently been introduced for monitoring NF-B profiles. The contribution made in this work is that the assumption that the transcription factor profile exhibits damped oscillations is relaxed, as transcription factors, other than the previously investigated NF-B, may exhibit different profiles. This is achieved by investigating a variety of potential profiles and solving the inverse problem for the model describing transcription, translation and activation of GFP for each one. The transcription factor profile that results in the best fit among the potential candidates, for the measured fluorescent intensity data, is then chosen as the most likely concentration profile. The technique is illustrated in two detailed case studies, where one case study involves simulation data whereas the other one uses experimentally derived fluorescent intensity data.

Anti-myelin antibodies modulate clinical expression of childhood multiple sclerosis

Anti-myelin basic protein (MBP) antibodies in pediatric-onset MS and controls were characterized. Serum samples were obtained from 94 children with MS and 106 controls. Paired CSF and serum were obtained from 25 children with MS at time of their initial episode of acute demyelinating syndrome (ADS). Complementary assays were applied across samples to evaluate the presence, and the physical binding properties, of anti-MBP antibodies. While the prevalence and titers of serum anti-MBP antibodies against both immature and mature forms of MBP were similar in children with MS and in controls, binding characteristics and formal Surface Plasmon Resonance (SPR) studies indicated surprisingly high binding affinities of all pediatric anti-MBP antibodies. Serum levels of anti-MBP antibodies correlated significantly with their CSF levels, and their presence in children with MS was associated with significantly increased risk of an acute disseminated encephalomyelitis-like initial clinical presentation. While antibodies to both immature and mature forms of MBP can be present as part of the normal pediatric humoral repertoire, these anti-myelin antibodies are of surprisingly high affinity, can access the CNS during inflammation, and have the capacity to modulate disease expression. Our findings identify an immune mechanism that could contribute to the observed heterogeneity in spectrum of clinical presentations in early-onset MS.

Xenogenic transplantation of human mesenchymal stem cells in a critical size defect of the sheep tibia for bone regeneration

Mesenchymal stem cells (MSCs) represent an attractive cell population for the regeneration of mesenchymal tissues. Their special immunological characteristics suggest that MSCs could be used in nonautologous applications. In this study, the regenerative capacity of human and ovine MSCs was assessed in an ovine critical size defect model. Human and ovine MSCs from bone marrow were cultured on mineralized collagen and implanted into a 3.0-cm-long sheep tibia bone defect (n = 7). Unloaded mineralized collagen served as control. Bone healing was assessed until euthanasia 26 weeks after surgery by radiology and histologically after euthanasia. The presence of human cells after xenogenic transplantation was analyzed using human-specific in situ hybridization. Both radiology and histology demonstrated significantly better bone formation after transplantation of autologous ovine MSCs on mineralized collagen compared with unloaded matrices and with the xenogenic treatment group. Nevertheless, no local or systemic rejection reactions could be observed after transplantation of human MSCs, although the presence of human MSCs could be demonstrated. It can be concluded that despite successful demonstration of the presence of human MSCs after xenogenic transplantation, the xenogenic transplantation of human MSCs leads to poorer bone regeneration than autologous transplantation of ovine MSCs.

Expanding CEP290 mutational spectrum in ciliopathies

Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert syndrome and related disorders (JSRD), Meckel syndrome (MKS), Senior-Loken syndrome and isolated Leber congenital amaurosis (LCA). Although these conditions are recessively inherited, in a subset of patients only one CEP290 mutation could be detected. To assess whether genomic rearrangements involving the CEP290 gene could represent a possible mutational mechanism in these cases, exon dosage analysis on genomic DNA was performed in two groups of CEP290 heterozygous patients, including five JSRD/MKS cases and four LCA, respectively. In one JSRD patient, we identified a large heterozygous deletion encompassing CEP290 C-terminus that resulted in marked reduction of mRNA expression. No copy number alterations were identified in the remaining probands. The present work expands the CEP290 genotypic spectrum to include multiexon deletions. Although this mechanism does not appear to be frequent, screening for genomic rearrangements should be considered in patients in whom a single CEP290 mutated allele was identified.

Recipient NOD2/CARD15 status affects cellular infiltrates in human intestinal graft-versus-host disease

Nucleotide-binding oligomerization domain 2/caspase recruitment domain 15 (NOD2/CARD15) polymorphisms have been identified as risk factors of both Crohn's disease and graft-versus-host disease (GVHD) following allogeneic stem cell transplantation. However, the role of these receptors of innate immunity in the pathophysiology of gastrointestinal GVHD is still poorly defined. Immunohistological features of intestinal GVHD were analysed in gastrointestinal biopsies from 58 patients obtained at the time of first onset of intestinal symptoms. The observed changes were correlated with concomitant risk factors and the presence of polymorphisms within the pathogen recognition receptor gene NOD2/CARD15. Intestinal GVHD was associated with a stage-dependent decrease in CD4 T cell infiltrates and an increase in CD8 T cells in the lamina propria; CD8 infiltrates correlated with extent of apoptosis and consecutive epithelial proliferation. The presence of NOD2/CARD15 variants in the recipient was associated with a significant loss of CD4 T cells: in a semiquantitative analysis, the median CD4 score for patients with wild-type NOD2/CARD15 was 1.1 (range 3), but only 0.4 (range 2) for patients with variants (P = 0.002). This observation was independent from severity of GVHD in multivariate analyses and could not be explained by the loss of forkhead box P3(+) T cells. Our results suggest a loss of protective CD4 T cells in intestinal GVHD which is enhanced further by the presence of NOD2/CARD15 variants. Our study might help to identify more selective therapeutic strategies in the future.

An in vivo evaluation of surface polishing of TAN intermedullary nails for ease of removal

Fractures of the tibia and femoral diaphysis are commonly repaired by intra-medullary (IM) nailing. Currently IM nails are available in either electropolished stainless steel (SS) or in Titanium-Aluminium-Niobium (TAN). After healing, removal of the nails still is common but removal of TAN IM nails often has complications whereas SS IM nails of the same design are less often associated with problems. We believe the differences in removal are due to the ability of TAN to promote strong bone on-growth. We have previously shown in vivo that polishing cortical screws reduces removal torque and the percentage of bone-implant contact. Therefore, we postulate that bony on-growth onto IM nails can be reduced by means of surface polishing, for ease of removal. Here we aim to compare the pull-out forces for removal of standard TAN (TAN-S) compared to experimental paste polished TAN (TAN-PP) IM nails from a bilateral non-fracture sheep tibia model after 12 months implantation. Histological analysis was also performed to assess tissue on-growth to the nails. We show that polishing significantly reduces (p=0.05) the extraction force required for TAN IM nail removal. This effect in part is attributable to the distinct tissue-material reaction produced. For TAN-S nails direct bone contact was observed while for TAN-PP nails a fibrous tissue interface was noted. Since TAN is preferred over SS for IM nailing due to superior biocompatibility and mechanical properties, we believe these findings could be used to recommend changes to current surface technologies of intramedullary nails to reduce complications seen with nail removal especially in rapidly growing bone in children.

Clinical spectrum of SIX3-associated mutations in holoprosencephaly: correlation between genotype, phenotype and function

BACKGROUND

Holoprosencephaly (HPE) is the most common structural malformation of the human forebrain. There are several important HPE mutational target genes, including the transcription factor SIX3, which encodes an early regulator of Shh, Wnt, Bmp and Nodal signalling expressed in the developing forebrain and eyes of all vertebrates.

OBJECTIVE

To characterise genetic and clinical findings in patients with SIX3 mutations.

METHODS

Patients with HPE and their family members were tested for mutations in HPE-associated genes and the genetic and clinical findings, including those for additional cases found in the literature, were analysed. The results were correlated with a mutation-specific functional assay in zebrafish.

RESULTS

In a cohort of patients (n = 800) with HPE, SIX3 mutations were found in 4.7% of probands and additional cases were found through testing of relatives. In total, 138 cases of HPE were identified, 59 of whom had not previously been clinically presented. Mutations in SIX3 result in more severe HPE than in other cases of non-chromosomal, non-syndromic HPE. An over-representation of severe HPE was found in patients whose mutations confer greater loss of function, as measured by the functional zebrafish assay. The gender ratio in this combined set of patients was 1.5:1 (F:M) and maternal inheritance was almost twice as common as paternal. About 14% of SIX3 mutations in probands occur de novo. There is a wide intrafamilial clinical range of features and classical penetrance is estimated to be at least 62%.

CONCLUSIONS

Our data suggest that SIX3 mutations result in relatively severe HPE and that there is a genotype-phenotype correlation, as shown by functional studies using animal models.

Neuronal activation in the nucleus of the solitary tract following jejunal lipopolysaccharide in the rat

INTRODUCTION

Inflammation during systemic lipopolysaccharide (LPS) seems to be modulated by the CNS via afferent and efferent vagal pathways. We hypothesized that similar to systemic inflammation, local LPS in the gut lumen may also activate central neurons and aimed to identify potential molecular mechanisms.

METHODS

Male Wistar rats were equipped with an exteriorized canula in the proximal jejunum. LPS or vehicle were administered into the jejunum (10 mg ml(-1)). For further study of molecular mechanisms, LPS or vehicle were administered systemically (1 mg kg(-1)). Brain stem activation was quantified by Fos-immunohistochemistry in the vagal nucleus of the solitary tract (NTS) and the Area postrema which is exposed to systemic circulation. Serum LPS concentrations were also determined.

RESULTS

Jejunal LPS exposure entailed 91+/-12 (n=7) Fos-positive neurons in the NTS compared to 39+/-9 in controls (n=6; p<0.01), while serum LPS concentrations and Fos-positive neurons in the Area postrema were not different. Systemic LPS triggered 150+/-25 (n=6) and vehicle 52+/-6 Fos-positive neurons (n=7; p<0.01). The Fos count after systemic LPS was reduced to 99+/-30 following pretreatment with the cyclooxygenase inhibitor Naproxen (10 mg kg(-1); p>0.05 versus vehicle controls) and increased to 242+/-66 following the iNOS-inhibitor Aminoguanidine (15 mg kg(-1); p<0.01). In the Area postrema, 97+/-17 (n=6) neurons were counted in animals pretreated with systemic LPS compared to 14+/-4 in controls (n=7, p<0.001).

CONCLUSIONS

Central neuronal activation following inflammation after systemic LPS is modulated by cyclooxygenase and NO pathways. Local exposure to bacterial LPS in the gut lumen activates the NTS which may set the stage for efferent vagal modulation of intestinal inflammation.

The role of genetic variants of NOD2/CARD15, a receptor of the innate immune system, in GvHD and complications following related and unrelated donor haematopoietic stem cell transplantation

Previous studies from our group indicated a role of SNPs within the innate immunity receptor NOD2/CARD15 as a risk factor for GvHD and treatment-related mortality allogeneic stem cell transplantation from HLA-identical siblings. We now extended these studies to assess the role of NOD2/CARD15 SNPs in 342 unrelated donor transplants. Overall, presence of any SNPs in patients or donor resulted in an increased risk of severe GvHD (25% in wildtype versus 38% in recipients and donors with variants, P= 0.01), which did not translate in increased mortality. When the analysis was broken down to individual SNPs, the presence of a SNP13 in the donor turned out to be the only highly significant risk factor (GvHD III/IV 22% wt, 42% SNP13 donor, P < 0.004; TRM 33% wt versus 59% SNP13 donor, P= 0.01; overall survival 49% wt versus 26% SNP13 donor, P= 0.007). This association was confirmed in multivariate analysis. Analysis of clinical risk factors suggested that this effect was most prominent in patients receiving any form of T cell depletion. Thus our observation indicates that the presence of a defect in innate immunity signalling in donor monocytes and possibly antigen presenting cells is most prominent in patients having additional T cell deficiency.

Coherent dynamics of self-induced ultraslow light for all-optical switching

Coherent dynamics of slow light for all-optical switching is investigated in a multilevel system of solids for an understanding of self-induced ultraslow light. In an optical population shelving system of a rare-earth doped solid, dynamics of the slow light are presented by using a third optical field controlling shelved atom population. Unlike two-photon coherence-based delayed all-optical switching utilizing electromagnetically induced transparency, the present method relies on one-photon coherence controlling shelved atom population.

Observations of self-induced ultraslow light in a persistent spectral hole burning medium

We present observations of self induced ultraslow light in a persistent spectral hole-burning rare-earth doped crystal. The observed group delay (velocity) is as long as 40 micros (75 m/s), which is comparable to that obtained using electromagnetically induced transparency or coherent population oscillations. We analyze the observed ultraslow light as a function of frequency detuning, light intensity, and atom population (oscillator strength). The present observation of ultraslow light in a persistent spectral hole-burning medium gives potentials to all-optical information processing such as on-demand all-optical buffer memories.

Parameter sensitivity analysis of IL-6 signalling pathways

Signal transduction pathways generally consist of a large number of individual components and have an even greater number of parameters describing their reaction kinetics. Although the structure of some signalling pathways can be found in the literature, many of the parameters are not well known and they would need to be re-estimated from experimental data for each specific case. However it is not feasible to estimate hundreds of parameters because of the cost of the experiments associated with generating data. Parameter sensitivity analysis can address this situation as it investigates how the system behaviour is changed by variations of parameters and the analysis identifies which parameters play a key role in signal transduction. Only these important parameters need then be re-estimated using data from further experiments. This article presents a detailed parameter sensitivity analysis of the JAK/STAT and MAPK signal transduction pathway that is used for signalling by the cytokine IL-6. As no parameter sensitivity analysis technique is known to work best for all situations, a comparison of the results returned by four techniques is presented: differential analysis, the Morris method, a sampling-based approach and the Fourier amplitude sensitivity test. The recruitment of the transcription factor STAT3 to the dimer of the phosphorylated receptor complex is determined as the most important step by the sensitivity analysis. Additionally, the desphosphorylation of the nuclear STAT3 dimer by PP2 as well as feedback inhibition by SOCS3 are found to play an important role for signal transduction.

Wie zuverlässig sind unsere Krebsstatistiken?

BACKGROUND

Among the causes of death, cancer ranks second after cardiovascular diseases. If a cancer patient dies before the tumor is diagnosed the malignancy may be unreported among post-mortem findings and thus is often not included in cancer and cause of death statistics.

METHOD

All 8844 autopsies carried out at the Institute of Forensic Medicine for the City of Hamburg from 1994 to 2001 were analysed and those cases with malignant tumor identified. The cases were then included in the cancer registry if this had not been done previously. The postmortem diagnosis of malignancy was made histologically on formalin-fixed tissue. In these cases attempts were made to find out if the initial diagnosis of malignancy had been made before death.

RESULTS

A malignancy was found in 519 autopsies (5.9 %). In 67.3 % of these (349/519) the patients had been aware of the disease. 27.2 % of all malignant tumors (141/519) were discovered during the post-mortem examination. In 5.6 % of cases (29/519) the question of whether the tumor had been diagnosed before death could not be answered because of lack of data or an incomplete case history. In 52.2 % (271/519) of the autopsies the tumor had definitely been the cause of death. Of these 271 tumors 17 % (46/271) were discovered only during the forensic post-mortem examination. The Hamburg Cancer Registry had been notified of only 58 cases of the 519. As a result of this study 451 new cancer cases (86.9 %) were notified to the Hamburg cancer registry.

CONCLUSIONS

The registration of cancer deaths in Hamburg is incomplete and the notification of cancer to the Cancer Registry is inadequate. The estimated number of unreported cases is probably greater and cancer as the cause of death is higher than reported in the statistics.

U19/Eaf2 knockout causes lung adenocarcinoma, B-cell lymphoma, hepatocellular carcinoma and prostatic intraepithelial neoplasia

Upregulated gene 19 (U19)/ELL-associated factor 2 (Eaf2) is a potential human tumor suppressor that exhibits frequent allelic loss and downregulation in high-grade prostate cancer. U19/Eaf2, along with its homolog Eaf1, has been reported to regulate transcriptional elongation via interaction with the eleven-nineteen lysine-rich leukemia (ELL) family of proteins. To further explore the tumor-suppressive effects of U19/Eaf2, we constructed and characterized a murine U19/Eaf2-knockout model. Homozygous or heterozygous deletion of U19/Eaf2 resulted in high rates of lung adenocarcinoma, B-cell lymphoma, hepatocellular carcinoma and prostate intraepithelial neoplasia. Within the mouse prostate, U19/Eaf2 deficiency enhanced cell proliferation and increased epithelial cell size. The knockout mice also exhibited cardiac cell hypertrophy. These data indicate a role for U19/Eaf2 in growth suppression and cell size control as well as argue for U19/Eaf2 as a novel tumor suppressor in multiple mouse tissues. The U19/Eaf2 knockout mouse also provides a unique animal model for three important cancers: lung adenocarcinoma, B-cell lymphoma and hepatocellular carcinoma.

Long-term surveillance of haematopoietic stem cell recipients with resolved hepatitis B: high risk of viral reactivation even in a recipient with a vaccinated donor

Reactivation of resolved hepatitis B virus (HBV) infection is increasingly recognized in patients with severe immunosuppression. We monitored seven patients with pretransplant antibodies to hepatitis B surface antigen (anti-HBs) and hepatitis B core antigen (anti-HBc) for HBV reactivation after allogeneic haematopoietic stem cell transplantation (allo-HSCT). Reverse seroconversion (from anti-HBs to HBsAg) was observed in six recipients occurring 12, 14, 16, 22, 31 and 39 months after allo-HSCT, respectively. The only patient without HBV reactivation had the highest pretransplant anti-HBs titre and died after the shortest follow-up period (25 months). A novel HBV surface mutant (D144G/G145E) was isolated from one recipient of stem cells from a donor vaccinated against HBV. Another surface mutant (P142L/G145R) was detected in a recipient from a non-immune donor. Serum ALT elevation was measured in only two of the six patients with viral reactivation, followed by spontaneous clearance of HBsAg in one of them. Antiviral treatment reduced viral load in five patients, but the emergence of YMDD motif polymerase mutations resulted in lamivudine resistance in two patients. In conclusion, the risk of reactivation of a resolved HBV infection is close to 100% in allogeneic stem cell recipients and vaccination of the donor does not always warrant reliable protection.

Alterations of neuropeptides in the human gut during peritonitis

BACKGROUND AND AIMS

Gastrointestinal motility is reduced during sepsis but the pathomechanism involved is poorly understood. We investigated the expression of substance P (SP) and vasoactive intestinal peptide (VIP) in the myenteric plexus during peritonitis in human small bowel.

MATERIALS AND METHODS

Tissue samples of the small bowel were gathered from healthy patients and from patients with peritonitis. Immunohistochemistry for myeloperoxidase (MPO), SP, and VIP was performed in whole mount sections. To determine the level of inflammation, MPO-positive cells were counted in the circular muscle layer. SP and VIP immunoreactivity was analyzed in myenteric plexus neurons. The area of positive immunoreactivity for either neuropeptide within the plexus was analyzed and set in relation to the total area of the plexus and consecutively expressed as percentage.

RESULTS

During peritonitis, MPO-positive cells significantly increased by approximately fourfold as compared to healthy tissue. The immunoreactivity for SP was significantly reduced by approximately 80% in myenteric plexus neurons during peritonitis. In contrast, the immunoreactivity for VIP significantly increased by nearly twofold during peritonitis.

CONCLUSIONS

During peritonitis, the inflammatory reaction within the gut is increased. The neuropeptide expression in myenteric plexus neurons was observed as shifting towards increased expression of VIP, known to inhibit intestinal motility, and towards decreased expression of the prokinetic neuropeptide SP.

Rotational spectroscopy of the isotopic species of silicon monosulfide, SiS

Pure rotational transitions of silicon monosulfide ((28)Si(32)S) and its rare isotopic species have been observed in their ground as well as vibrationally excited states by employing Fourier transform microwave (FTMW) spectroscopy of a supersonic molecular beam at centimetre wavelengths (13-37 GHz) and by using long-path absorption spectroscopy at millimetre and submillimetre wavelengths (127-925 GHz). The latter measurements include 91 transition frequencies for (28)Si(32)S, (28)Si(33)S, (28)Si(34)S, (29)Si(32)S and (30)Si(32)S in upsilon = 0, as well as 5 lines for (28)Si(32)S in upsilon = 1, with rotational quantum numbers J''< or = 52. The centimetre-wave measurements include more than 300 newly recorded lines. Together with previous data they result in almost 600 transitions (J'' = 0 and 1) from all twelve possible isotopic species, including (29)Si(36)S and (30)Si(36)S, which have fractional abundances of about 7 x 10(-6) and 4.5 x 10(-6), respectively. Rotational transitions were observed from upsilon = 0 for the least abundant isotopic species to as high as upsilon = 51 for the main species. Owing to the high spectral resolution of the FTMW spectrometer, hyperfine structure from the nuclear electric quadrupole moment of (33)S was resolved for species containing this isotope, as was much smaller nuclear spin-rotation splitting for isotopic species involving (29)Si. By combining the measurements here with previously published microwave and infrared data in one global fit, an improved set of spectroscopic parameters for SiS has been derived which include several terms describing the breakdown of the Born-Oppenheimer approximation. With this parameter set, highly accurate rotational frequencies for this important astronomical molecule can now be predicted well into the terahertz region.

Glycoprotein IIb/IIIa inhibitor-induced thrombocytopenia

Thrombocyte glycoprotein IIb/IIIa inhibitors prevent fibrinogen binding and thereby thrombocyte aggregation. The inhibition of thrombocyte activation at the damaged coronary plaque is the target of the new therapeutic strategies in treating acute coronary syndrome. This reduces the ischemic complications associated with the non-STelevation myocardial infarction (NSTEMI) and percutaneous coronary intervention (PCI). Thrombocytopenia is a known complication of glycoprotein (GP) IIb/IIIa inhibitors. Although, in general, GP IIb/IIIa inhibitor-induced thrombocytopenia is a harmless side effect which responds readily to thrombocyte transfusion, it can occasionally be a very serious complication associated with serious bleeding. In addition patients developing thrombocytopenia have unfavorable outcome (e.g., death, myocardial infarction, bypass surgery or additional PCI) in comparison to patients without thrombocytopenia. Advanced age (> 65 years), low BMI and a low initial thrombocyte count (<180,000/microl) are independent risk factors of thrombocytopenia. The risk of bleeding is higher with this form of thrombocytopenia not only due to the low thrombocyte count but also to the impaired function of the remaining thrombocytes. It is important to closely monitor platelet count during GP IIb/IIIa antagonist treatment. Platelet count monitoring two, six, twelve and 24 hour after starting the treatment reveals most cases of acute thrombocytopenia. Side effects can be avoided by the early discontinuation of the GP IIb/IIIa antagonist treatment. This article reviews the diagnosis and treatment of glycoprotein IIb/IIIa inhibitor-induced thrombocytopenia and summarizes the differential diagnosis from heparin-induced thrombocytopenia and laboratory-related pseudothrombocytopenia.