Site-independent prognostic value of chromosome 9q loss in primary gastrointestinal stromal tumours

Although the significance of tumour site for estimating malignant potential in gastrointestinal stromal tumours (GISTs) has recently been recognized, site-specific genetic patterns have not to date been defined. This study examined 52 c-kit-positive primary GISTs (with a mean follow-up of 42.3 months in 51 cases) from three different locations (35 gastric, 12 small intestinal, and five colorectal) using comparative genomic hybridization (CGH). In general, tumour site correlated with key prognostic factors, including tumour size, mitotic rate, proliferative activity, and probable malignant potential. Furthermore, several DNA copy number changes showed a site-dependent pattern. These included losses at 14q (gastric 83%, intestinal 35%; p = 0.001), losses at 22q (gastric 46%, intestinal 82%; p = 0.02), losses at 1p (gastric 23%, intestinal 88%; p = 1 x 10(-5)), losses at 15q (gastric 14%, intestinal 59%; p = 0.002), losses at 9q (gastric 14%, intestinal 53%; p = 0.006), and gains at 5p (gastric 11%, intestinal 53%; p = 0.002). These data demonstrate strong site-dependent genetic heterogeneity in GISTs that may form a basis for subclassification. Prognostic evaluation of DNA copy number changes identified losses at 9q as a site-independent prognostic marker associated with shorter disease-free survival (p = 0.03) and overall survival (p = 0.002). Furthermore, 9q loss also appeared to carry prognostic value in predicting overall survival for patients with advanced or progressive GISTs (p = 0.003).     

Microstructural disassembly of calcium phosphates

Microstructural factors may play a role in the osseointegration of calcium phosphates. In this paper, direct microstructural interactions between crystalline calcium phosphates and the biological milieu are reported. Degradation via exposure to osteoblast culture closely resembles in vivo interactions with subcutaneous tissues in a bovine model at early time periods. That these interactions were common to both experiments constitutes one of the few known examples of in vitro-in vivo correspondence. Interestingly, the degradation of phase pure hydroxyapatite (HA) in vitro was more rapid than that of biphasic HA in vivo. In both cases, grain extraction/pullout was frequently observed. This suggests a connection to smaller-scale observations of epitaxial CHA nucleation and growth on pre-existing HA grains. A microstructure in which the grain boundary is dissolving/corroding can apparently be disassembled by forces transmitted through biological structures. These observations are distinct from those of simple non-biological solutions and prove that biological environments can interact with the material beneath the ceramic-cell/ceramic-tissue interface. Many often ignored microstructural factors-grain size, shape, grain boundary strength and the presence of impurity phases-may in fact control degradation. We also suggest that even relatively modest initial grain sizes will, in combination with the mild/absent foreign body response to calcium phosphates, result in lengthy in vivo particle resistence.     

Use of in vivo-induced antigen technology for identification of Escherichia coli O157:H7 proteins expressed during human infection

Using in vivo-induced antigen technology (IVIAT), a modified immunoscreening technique that circumvents the need for animal models, we directly identified immunogenic Escherichia coli O157:H7 (O157) proteins expressed either specifically during human infection but not during growth under standard laboratory conditions or at significantly higher levels in vivo than in vitro. IVIAT identified 223 O157 proteins expressed during human infection, several of which were unique to this study. These in vivo-induced (ivi) proteins, encoded by ivi genes, mapped to the backbone, O islands (OIs), and pO157. Lack of in vitro expression of O157-specific ivi proteins was confirmed by proteomic analysis of a mid-exponential-phase culture of E. coli O157 grown in LB broth. Because ivi proteins are expressed in response to specific cues during infection and might help pathogens adapt to and counter hostile in vivo environments, those identified in this study are potential targets for drug and vaccine development. Also, such proteins may be exploited as markers of O157 infection in stool specimens.     

Detection of Pseudomonas aeruginosa producing metallo-beta-lactamases in a large centralized laboratory

Metallo-beta-lactamases (MBLs) have been increasingly recognized from clinical isolates worldwide, but the laboratory detection of these strains is not well defined. We report a study that developed an EDTA disk screen test and a molecular diagnostic assay for the detection of MBL-producing Pseudomonas aeruginosa. Using NCCLS disk methodology, inhibition zone diameters were determined in tests with imipenem (IPM) and meropenem (MEM) disks alone and in combination with 930 microg of EDTA. This test was compared with the MBL Etest. The duplex PCR assay showed 100% sensitivity and specificity for detecting MBL-producing control strains. Of the 241 clinical strains of IPM-nonsusceptible P. aeruginosa from the Calgary Health Region isolated from 2002 to 2004, 110/241 (46%) were MBL positive using phenotypic methods while 107/241 (45%) were PCR positive for MBL genes: 103/241 (43%) for bla(VIM) and 4/241 (2%) for bla(IMP). The EDTA disk screen test using MEM showed 100% sensitivity and 97% specificity for detecting MBLs in control and clinical strains. The EDTA disk screen test is simple to perform and to interpret and can easily be introduced into the workflow of a clinical laboratory. We recommend that all IPM-nonsusceptible P. aeruginosa isolates be routinely screened for MBL production using the EDTA disk screen test and that PCR confirmation be performed at a regional laboratory.     

Age-related differences in novelty and target processing among cognitively high performing adults

Previous research on age-related changes in ERP components in response to novel and target stimuli has not carefully controlled for differences in level of cognitive status between age groups, which may have contributed to the common findings of increased P3 latency, decreased P3 amplitude, and altered P3 scalp distribution. Here, cognitively high-performing (top third based on published norms) old, middle-aged, and young adults matched for IQ, education, and gender participated in a novelty oddball paradigm. There were no age-associated differences in P3 latency. Older adults had a larger, more anteriorly distributed P3 amplitude to all stimulus types, even repetitive standards, suggesting they may rely on increased resources and effortful frontal activity to successfully process any kind of visual stimulus. However, after controlling for this non-specific age-related processing difference, the amplitude and scalp distribution of the P3 component to novel and target stimuli were comparable across age groups, indicating that for cognitively high functioning elders there may be no age-related differences specific to the processing of novel and target events as indexed by the P3 component.     

Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays

Use of sequencing-based genotyping as a diagnostic assay for human immunodeficiency virus (HIV) antiretroviral resistance is increasing. Periodic evaluation of the proficiency of laboratories performing this assay should be established. It is important to identify components of the assay that influence the generation of reliable sequencing data and that should and can be monitored. A model was developed to determine what parameters were reasonable and feasible for assessing the performance of genotyping assays. Ten laboratories using the genotyping platform, HIV-1 Genotyping System (HGS) v. 1 and software versions 1.1 or 2.0, participated in two rounds of testing. For each round, each group was sent a panel consisting of three clinical samples to sequence in real time. Six months later, seven laboratories using the TRUGENE HIV-1 Genotyping Kit participated in a separate round, working with both panels at the same time. Analysis of the data showed that one main indicator of genotyping proficiency was achievement of > or =98% sequence homology of a sample tested to a group consensus sequence for that sample. A second was concordant identification of codons at sites identified with resistance mutations in the sample, although scoring of these criteria is still undetermined from this study. These criteria are applicable to all sequence-based genotyping platforms and have been used as a baseline for assessing the performance of genotyping for the determination of antiretroviral resistance in our ongoing proficiency program.     

Responses against complex antigens in various models of CD4 T-cell deficiency

The most common models of CD4 T-cell deficiency are mice exogenously injected with anti-CD4 antibody (Ab), CD4 knockout (CD4^−/−) and major histocompatibility complex (MHC) class II knockout (class II^−/−) mice. We recently described the anti-CD4 Ab transgenic mouse (GK) as an improved CD4 cell-deficient model. This review compares this new GK mouse model with the widely available class II^−/− and CD4^−/− mice, when exposed to complex antigens (foreign grafts and during bacterial or viral infection). We highlight here the cytometric and functional differences (including Ab isotype, viral or bacterial clearance, and graft survival) among these CD4 cell-deficient models. For example, whereas grafts are generally rejected in class II^−/− and CD4^−/− mice as quickly as in wild-type mice, they survive longer in GK mice. Also, CD4^−/− mice produce IgG against both simple model and complex antigens, but class II^−/− and GK mice produce small amounts of IgG2a against complex antigens but not simple model antigens. These differences harbinger the caveats in the use of these various mice.     

Inter- and intra-muscle comparisons of MAPK mechanosensitivity: evidence for the absence of fibre-type dependency

Muscle phenotype is regulated by mechanical forces. However, it is not well understood how these forces are translated into intracellular signalling that influences gene expression. The purpose of this study was to test the hypothesis that muscles displaying a wide range of metabolic profiles and fibre-type composition exhibit differences in the detection and transmission of mechanical stimuli. A mechanical challenge in the form of passive stretch normalized to 3 N/g muscle weight was applied to the rat extensor digitorum longus (EDL), soleus (SOL), and plantaris (PLN) in situ for 5 min, following which activities of the mechanically-responsive p54 c-jun NH(2)-terminal kinase (JNK) and extracellular-regulated kinase (ERK) 1/2 were measured. EDL, SOL, and PLN were not different in their stretch-induced JNK (4.5, 5.2 and 6-fold baseline, respectively) or ERK (2.2, 2.2 and 1.9-fold baseline, respectively) responses, in spite of differing fibre-type compositions. The medial gastrocnemius (MG), a compartmentalized muscle with red (MGr) and white (MGw) regions, was subjected to the same normalized mechanical stretch protocol. The resulting JNK and ERK activities were significantly higher in MGr (13 and 4.5-fold baseline, respectively) than in MGw (5 and 1.2-fold baseline, respectively) and all other muscles. In contrast to stimulation by passive stretch, stimulation of the MG by isometric contractile activity did not result in a heterogeneous response between compartments. This study demonstrates an absence of difference among muscles of varying phenotype in their ability to transmit mechanical stimuli to the mitogen-activated protein kinase signalling pathways, and hence in their mechanosensitivity. Furthermore, the results highlight the importance of considering aspects of the functional organization of different muscles, such as compartmentalization and architecture, when studying mechanical signalling in vivo.     

Accumulation of p53 in response to adenovirus early region 1A sensitizes human cells to tumor necrosis factor alpha-induced apoptosis

Many tumor cells are resistant to tumor necrosis factor alpha (TNFalpha)-induced apoptosis. Adenovirus early region 1A (AdE1A) sensitizes the otherwise resistant cells to TNFalpha. AdE1A also stabilizes the p53 protein. The present study demonstrates a correlation between AdE1A-induced sensitization and stabilization of p53 in TNFalpha-induced apoptosis since the N-terminal and CR2 regions, the binding sites for CBP/p300, Rb and 26S proteasome regulatory components, are required for both these actions of AdE1A. TNFalpha does not induce apoptosis and AdE1A fails to sensitize TNFalpha cytotoxicity in p53-negative cells. However, introduction of exogenous p53 overcomes the cellular resistance to TNFalpha toxicity and enhances AdE1A sensitization, demonstrating that AdE1A sensitizes TNFalpha-induced apoptosis by its stabilization of p53. A proteasome inhibitor, lactacystin, enhances TNFalpha cytotoxicity in p53-positive and -negative cells, suggesting that accumulation of cellular proteins other than p53 might also regulate the cellular response to TNFalpha signaling.     

Viral nucleic acid sequences in transformed cells: IV. A study of the sequences of adenovirus 5 DNA and RNA in four lines of Adenovirus 5-transformed rodent cells using specific fragments of the viral genome

Specific fragments of Adenovirus 5 DNA were produced by digestion of intact, ³²P-labeled viral DNA with restriction endonucleases Eco R1 and and Hpa 1. The kinetics of renaturation of each fragment and of complete Adenovirus 5 DNA were measured in the presence of DNA extracted from four lines of Adenovirus 5-transformed rodent cells and from nontransformed control cells. All four transformed cell lines contained sequences homologous to the Hpa 1 fragment comprising the left 4% of the viral genome, but varied in the other Adenovirus 5 DNA sequences which were present: three lines of transformed cells contain segments of DNA extending from the left hand end to points 35, 40, and 12% along the viral genome and carry no other Adenovirus 5 DNA sequences. The fourth line also contains sequences homologous to the left half of the viral genome, but these could not be precisely defined. Therefore, the gene(s) encoded by the left end of Adenovirus 5 DNA must specify any viral gene functions expressed in transformed cells.Separated strands of the three Eco R1 fragments and certain Hpa 1 fragments of ³²P-labeled Adenovirus 5 DNA were hybridized with unlabeled, cytoplasmic RNA extracted from each of the four transformed cell lines. In each case, about 10% only of the r strand sequences of the largest Eco R1 fragment were complementary to transformed cell RNA. These sequences have been mapped to the left end of the viral genome using Hpa 1 fragment strands. The same sequences are shown to be expressed as mRNA during the early phase of an Adenovirus 5 lytic infection.