Founded in 1962 and, therefore, the oldest international journal in medical informatics, Methods of Information in Medicine will publish its 50th volume in 2011. At the start of the journal's sixth ...decade, a discussion on the journal's profile seems appropriate.
To report on the new opportunities for online access to Methods publications as well as on the recent strategic decisions regarding the journal's aims and editorial policies.
Describing and analyzing the journal's aims and scope. Reflecting on recent publications and on the journal's development during the last decade.
From 2011 forward all articles of Methods from 1962 until the present can be accessed online. Methods of Information in Medicine stresses the basic methodology and scientific fundamentals of processing data, information and knowledge in medicine and health care. Although the journal's major focus is on publications in medical informatics, it has never been restricted to publications only in this discipline. For example, articles in medical biometry, in or close to biomedical engineering, and, later, articles in bioinformatics continue to be a part of this journal.
There is a continuous and, as it seems, ever growing overlap in the research methodology and application areas of the mentioned disciplines. As there is a continuing and even growing need for such a publication forum, Methods of Information in Medicine will keep its broad scope. As an organizational consequence, the journal's number of associate editors has increased accordingly.
Previously we have reported about human nuclear matrix proteins (hNMPs) with increased reassembling and potential filament-forming capability C. Gerner et al., 1999, J. Cell. Biochem. 74, 145–151. ...Here, we cloned the cDNA of one of these proteins, hNMP 200, following partial amino acid sequencing of the novel 56-kDa nuclear protein. Sequence alignments show hNMP 200-related proteins in metazoans, plants, and yeast, the homologous Saccharomyces cerevisiae protein prp19 being an accessory, but essential, factor for pre-mRNA processing. Evidence for any enzymatic activity was not detected. However, the hNMP 200 primary sequence contained five consensus WD-repeat sequences, indicative of participation and regulatory function in larger protein assemblies. Northern blot analysis and 2D protein electrophoresis showed ubiquitous expression of hNMP 200 in a variety of cell types. 35S labeling studies indicated a high metabolic stability of the protein. The hNMP 200 gene was assigned to chromosomal region 11q12.2. Confocal laser scanning microscopy revealed that the intracellular localization conformed with that reported for other structural nuclear proteins. In interphase cells, green fluorescent protein-tagged hNMP 200 was predominantly nucleoplasmic. Structures with speckled appearance extended through several sections of in situ-isolated nuclear matrices. During cell division hNMP 200 became irregularly distributed in prophase, sparing regions of condensing chromatin. In anaphase it was concentrated in the spindle midzone. The putative dual function of the novel NMP is discussed. Being a component of the nuclear framework, it may provide structural support for components of the RNA-processing machinery, thereby also modulating splicing activities.
Hepatitis C virus (HCV) infection is a major cause of liver cirrhosis and hepatocellular carcinoma. Within days post infection, innate immunity is activated by HCV reflected by an induction of ...IFN-stimulated genes (ISGs). The precise cell type and cellular pathogen pattern recognition receptors (PRRs) involved in innate immune sensing of HCV, however, still remain unknown.
To study this as close as possible to the physiological situation, we utilized ex vivo perfused human liver tissue. By pulse perfusing the liver with HCV for 1h and chase perfusing the liver with HCV free media for 23h, we found the virus after 1h predominantly in sinusoidal endothelial cells and kupffer cells(KC). After 23h chase perfusion, HCV could be found in hepatocytes. When hepatic RNA was extracted after 48h perfusion, induction of IFN was detected by real time RT-PCR.
To investigate if TLRs are involved in HCV recognition, we isolated LSEC, KC and hepatocytes from human liver tissue resections, and compared the TLRs expression levels to circulating immune cells by real time RT-PCR. TLR3 was found to be highly expressed in LSEC, KC and hepatocytes. Cytokine secretion after poly (I:C) stimulation confirmed functionality of TLR3 in KC and LSEC, but revealed that TLR3 has lower functionality in hepatocytes. This could be explained by low expression levels of central adaptors TRIF, RIP1 and RIP3 in the TLR3 signaling cascade in hepatocytes.
Thus, we hypothesized that TLR3 might mediate activation of innate immunity against HCV. Since TLR3 is highly conserved from mouse to human and shares structural and functional similarities, we utilized mouse models to verify our hypothesis. Using purified mouse LSEC in vitro, we detected mouse IFN-beta induction by real-time RT-PCR 6h after HCV stimulation. When we perfused mouse liver with HCV we found that – as in human tissue – the virus predominantly localized in mouse LSECs after 1h. When comparing wild type to TLR3-/- CH57Bl/6 mice, perfusion with HCV induced IFN only in wild type mice but not in knock out mice.
From these data we conclude that HCV particles entering the liver are largely endocytosed by LSECs and KCs. In the liver sinusoid, TLR3 senses HCV in LSECs and KCs and induces IFN expression contributing to early immune activation.
Corresponding author:
Protzer, Ulrike
E-Mail:
Ulrike.Protzer@tum.de
Abstract 849
Core-binding-factor (CBF) acute myeloid leukemia (AML) defined by the presence of t(8;21)(q22;q22) or inv(16)(p13.1q22)/t(16;16)(p13.1;q22) is associated with favorable outcome. However, ...about 30–40% of patients are not cured by current treatment approaches. Secondary genetic changes are believed to cause clinical heterogeneity. To identify new secondary genetic lesions, we performed high-resolution, genome-wide analysis of copy number aberrations (CNA) and copy neutral loss of heterozygosity (CN-LOH) using Affymetrix 6.0 single nucleotide polymorphism (SNP) microarrays in 300 adult and pediatric CBF AMLs; t(8;21), n=157 (adult, n=114; pediatric, n=43); and inv(16), n=143 (adult, n=104; pediatric, n=39). Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 175 patients. In addition, for 42 patients matched relapse samples were analyzed. Data were processed using reference alignment, dChipSNP and circular binary segmentation. Paired analysis revealed a median of 1.28 somatic CNAs per case t(8;21): 1.14, range: 0–5; inv(16): 1.45, range: 0–9, with deletions more common than gains t(8;21): 0.94 losses/case vs. 0.2 gains/case; inv(16): 0.95 vs. 0.5. Recurrent deletions were detected at chromosomal bands 7q36.1 (n=23), 9q21.13 (n=15), 11p13 (n=7), 17q11.2 (n=6), 10q24.32 (n=2), and at the chromosomal breakpoints of t(8;21) and inv(16) on 8q21.3 (n=9), 21q22 (n=16), 16p13.11 (n=28), and 16q22.11 (n=21). Deletions at 7q, 11p and 17q were validated using FISH analysis. Minimally deleted regions (MDR) less than 1.5 Mb were identified at 7q36.1 (647 Kb, 4 genes), 9q21.13 (1125 Kb, 9 genes), 11p13 (130 Kb, 1 gene), and 17q11.2 (902 Kb, 11 genes), with each region containing a putative tumor suppressor (e.g., MLL3 on 7q, FRMD3 on 9q, WT1 on 11p, and NF1 on 17q). Sequence analysis of MLL3 in 23 cases with del(7q), 1 case with 7q CN-LOH, and 23 randomly selected cases identified a MLL3 truncating mutation leading to a premature stop codon in a case that lacked a 7q alteration. The del(11p13) contained only WT1 and primarily affected inv(16)-cases (5 of 7). Sequence analysis of WT1 in four cases with del(11p) revealed an additional frame shift mutation in the remaining allele in one case. Sequence analysis of WT1 in an additional 103 inv(16)-containing cases revealed mutations in 10 (9%) of the cases. The MDR at 17q11.2 was exclusively identified in inv(16)-containing cases (n=6) and included the tumor supressor NF1. Sequence analysis of all coding exons in NF1 in 4 additional inv(16)-containing AMLs revealed no additional mutation. Recurrent gains were identified at 22q11.21-q13.33 (n=20; 32 Mb), 8q24.21 (n=14; 138 Kb), 13q21.1-q34 (n=6; 14 Mb), and 11q25 (n=5; 368 Kb). The smallest gains were identified at 8q24.21 and 11q25, both containing only a single non-coding RNA gene (CCDC26 and LOC283177, respectively). Somatic CN-LOH were uncommon and only found at 1p36.33-p12 (n=2), 4q (n=2), and 19p (n=2). In a comparative analysis of paired diagnostic and relapse samples, novel CNAs at the time of relapse were identified at 3q13.31 (n=5), 5q (n=2), 17p (n=2), and 17q (n=2). The MDR at 3q was only 46 kb in size and contains a single transcript that has been connected to LSAMP, a putative tumor suppressor located 404 Kb upstream of the deletion. In summary, our data provide a comprehensive profiling of copy number alterations in pediatric and adult CBF AML. These data demonstrate a very low number of CNAs, with no significant differences noted between pediatric and adult cases. Interestingly, a number of novel recurrent secondary genetic alterations are identified. Exploring the biological role of these lesions in leukemogenesis and drug resistance should provide important insights into the CBF leukemias.
No relevant conflicts of interest to declare.
The clinical management of pancreatic disease is often hampered by a lack of tissue diagnosis. Endoscopic pancreatography offers the opportunity to investigate exfoliated cells. However, the ...significance of mere cytological investigation is compromised by an insufficient sensitivity. The evaluation of the molecular background of carcinogenesis hopefully is capable of providing more sensitive diagnostic markers. The p16INK4a-/retinoblastoma tumour-suppressive pathway has been shown to be involved in the development of near to all pancreatic neoplasms. p14ARF is another tumour suppressor located in the immediate neighbourhood of p16INK4a. Promoter methylation has been demonstrated to be a major inactivating mechanism of both genes. We sought to further evaluate the role of the gene locus INK4a methylation status in the endoscopic differentiation of chronic inflammatory and neoplastic pancreatic disease. Pancreatic fluid specimens of 61 patients with either pancreatic carcinoma (PCA: 39), chronic pancreatitis (CP: 16) or a normal pancreatogram (NAD: 6) were retrieved. In order to detect methylation of either the p14ARF or the p16INK4a promoter a methylation-specific PCR protocol was applied. While 19 out of 39 patients with PCA showed p16 promoter methylation (49%), none of the 16 patients with CP revealed p16 promoter methylation. p14ARF methylation was found in a lower percentage of PCA specimens and in none of the samples of patients with CP. These results suggest a specific significance of INK4a for the development of malignant pancreatic disease. Our data further indicate a potential role for INK4a methylation as a diagnostic marker in the endoscopic differentiation of benign and malignant pancreatic disease.
Objective:
In a previously published prospective controlled cohort study, thymectomized children, who had thymectomy in early childhood due to open heart surgery, completed a three-dose immunization ...regimen in order to analyze the clinical impact of immunological alterations in thymectomized patients after exposure to a new antigen (tick-borne encephalitis virus (TBEV) vaccine). In the previous study, thymectomized children showed significantly lower TBEV IgG antibody levels after the second vaccination when compared to healthy age-matched controls, but a normal response after the third vaccination.
Methods:
The present study was aimed to analyze the TBEV-specific IgG antibody response 3 years after the third TBE vaccination in 22 thymectomized patients compared to 37 non-thymectomized healthy controls from the previously published cohort, to identify patients with waning antibody titers. Additionally, the serum samples were tested for measles, mumps and rubella IgG antibody concentrations after immunization with live-virus-attenuated vaccine administered post thymectomy. The TBEV-, measles- und rubella-specific IgG antibody avidity was analyzed by an adapted ELISA.
Results:
Although there was a great inter-individual variety in the TBEV-specific IgG concentrations, thymectomized patients showed equal levels compared to healthy controls. The humoral immune response to measles, mumps and rubella was normal in thymectomized patients. There was no difference in avidity maturation of TBEV-, measles- und rubella-specific IgG antibodies between patients and healthy controls.
Conclusion:
Despite a delayed primary humoral immune response to new vaccine antigens, thymectomized patients are able to produce and maintain an appropriate memory immune response to TBEV vaccine and live-virus-attenuated vaccines administered post thymectomy. These follow-up data underline the hypothesis of a normal memory function but a diminished primary humoral immune response to new antigens in thymectomized patients, which may also have an impact in later life with increased risk of morbidity or mortality due to infectious diseases with new pathogens.
Mutations in two genes, α-synuclein and parkin, have been identified as some rare causes for familial Parkinson’s disease (PD). α-Synuclein and parkin protein have subsequently been identified in ...Lewy bodies (LB). To gain further insight into the pathogenesis of PD we investigated the role of neurofilament light (NF-L), another component of LB aggregation. A detailed mutation search of the NF-L gene in 328 sporadic and familial PD patients of German ancestry revealed three silent DNA changes (G163A, C224T, C487T) in three unrelated patients. Analysis of the promoter region of the NF-L gene identified a total of three base pair substitutions defining five haplotypes. Association studies based on these haplotypes revealed no significant differences between PD patients and 344 control individuals. Therefore, NF-L is unlikely to play a major role in the pathogenesis of PD.
By systematic comparison of two-dimensional electrophoretic patterns of nuclear matrix proteins an ubiquitously occurring (common) nuclear matrix protein, termed NMP 238, was detected. Localization ...of the protein in isolated nuclear matrices and in nuclear and cytoplasmic regions of cells was determined by confocal immunofluorescence microscopy. N-terminal protein sequencing, mass spectrometry, and sequencing of a human EST cDNA clone showed identity of the protein with a nuclear protein, termed TIP49, of as yet uncertain function. Expression of the corresponding gene in diverse human and rat cells was confirmed by Northern blotting. The protein displays two nuclear localization signals. Sequence homologies indicate evolutionary related proteins in nematodes, yeast, and archaebacteria. Similarities to the AAA family of proteins and to a subgroup of chaperones suggest that the nuclear matrix protein may play a role in the assembly and ATP-dependent anchorage of proteins.
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