Competitive displacement of DNA during surface hybridization

Using real-time dual-color fluorescence detection, we have experimentally tracked individual target species during competitive DNA surface hybridization in a two-component sample. Our experimental results demonstrate displacement of the lower affinity species by the higher affinity species and corroborate recent theoretical models describing competitive DNA surface hybridization. Competition at probe sites complementary to one of the two DNA species was monitored in separate experiments for two different target pairs. Each pair differs in sequence by a single nucleotide polymorphism, and one pair includes a folding target. We propose a mechanistic interpretation of the differences between hybridization curves of targets in multi-component and single-component experiments.

beta-Catenin/Wnt signaling regulates expression of the membrane type 3 matrix metalloproteinase in gastric cancer

Activation of Wnt signaling through beta-catenin dysregulation occurs in numerous human tumors, including gastric cancer. The specific consequences of Wnt signaling in gastric cancer, however, are not well characterized. This study shows that the introduction of mutant beta-catenin into gastric cancer cell lines by adenoviral infection enhances invasiveness and proliferation and up-regulates the expression of the gene encoding the matrix metalloproteinase (MMP) family member membrane type 3 MMP (MT3-MMP). Up-regulation of MT3-MMP is critical to the invasive phenotype as shown by small interfering RNA (siRNA) studies. Immunohistochemical staining also showed that MT3-MMP was highly expressed in gastric cancers with activating beta-catenin mutations. These observations suggest that Wnt activation may contribute to gastric cancer progression by increasing the invasiveness of neoplastic cells in the stomach via up-regulation of MT3-MMP expression.

Radiotherapy plus concurrent irinotecan (CPT-11) and capecitabine (CAP) as preoperative downstaging treatment for locally advanced inoperable rectal cancer: A phase I/II study

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Background: Preoperative downstaging chemoradiation has become standard treatment for locally advanced unresectable rectal cancer. Oral CAP is potentially more convenient as a radiation sensitiser than infusional fluoropyrimidine regimes. This study evaluated the dose-limiting toxicity (DLT), maximum tolerated dose (MTD) and recommended dose (RD) of daily CAP plus weekly i.v. CPT-11 when used in combination with RT in locally advanced rectal cancer. Methods: Patients had an adenocarcinoma of the rectum (lower limit within 12 cm of the anal verge) which on MRI was T3 within 2 mm of the mesorectal outer edge, T4, or any T3 within 5 cm of the anal verge. There were no distant metastases on staging investigations. Patients received planned pelvic RT to 45 Gy in 25 daily fractions over five weeks, concurrent with oral CAP daily throughout RT (including weekends) and a 60 minute infusion of i.v. CPT-11 weeks 1, 2, 3 and 4. Doses of CAP and CPT-11 were gradually escalated in cohorts of three patients. Results: The most common DLT was diarrhoea. Initially dose level (D/L) 3 was chosen as the recommended dose for phase II. However, unacceptable toxicity was encountered in the first 12 patients treated at D/L 3 (see Table). Thus D/L 2 is now being expanded to 60 patients for phase II. 40 patients have thus far potentially been eligible for resection: 5 (13%) could not be resected (2 deteriorated, 2 developed metastases, 1 died during treatment), 32 (80%) had R0 and 3 (7%) R1 resection. 9 (25%) had a pathological complete response (pCR) and 7 (20%) ‘near’ pCR. 5 (9%) of 57 patients had a defunctioning stoma pre-RT. Conclusions: The RD for this regime is 60 mg/m2 i.v. CPT-11 weeks 1, 2, 3, 4 and 650 mg/m2 bd of oral CAP daily. This demonstrates promising signs of efficacy. The RD is currently being studied in an expanded phase II cohort of 60 patients. D=diarrhea; F=febrile neutropenia; A=anorexia; L=lethargy; N=nausea/vomiting. [Table: see text]

No significant financial relationships to disclose.

Effects of fill fraction on the capture efficiency of nanoscale molecular transducers

We study the effects of nanotransducer fill fraction on the molecular capture efficiency contribution to overall sensor response. Contrary to expectation, we show that the relative capture efficiency can exceed the fill fraction in the transient regime. However, at thermodynamic equilibrium, the relative efficiency equals the fill fraction in the probe-limited case. When the number of target molecules in solution is the limiting factor in capture, then gains in capture efficiency can be obtained even at thermodynamic equilibrium. The important implication of these results is that significant intrinsic nanotransducer enhancement is necessary in order to provide net gain in sensor response, but that nanotransducer enhancement does not need to exceed the inverse fill fraction. In addition, net gain in overall sensor response is more readily achievable at low target concentrations.

A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants

Microarray analysis has become increasingly complex due to the growing size of arrays and the inherent cross-binding of targets. In this work, we explore the effects of matched and mismatched target species concentrations, temperature, and the time of hybridization on sensing specificity in two-component systems. A finite element software is used to simulate the diffusion of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. Comparison between a single-component system, where only one target is allowed to bind to a specific zone, and a two-component system, where more than one target can hybridize in a sensing zone, uncovers significant kinetic disparities during the transitory state; however, at thermodynamic equilibrium a modified Langmuir isotherm governs the bound amount of both species. The results presented suggest that it may be more appropriate to consider collective rather than quasi-independent interaction of targets in multicomponent systems.

Flammability of Common Ocular Lubricants in an Oxygen-Rich Environment

PURPOSE

Approximately 100 surgical fires take place in the United States each year. Recently, an ophthalmic lubricant was blamed for burning a child's eye while oxygen was administered during surgery. This study sought to determine whether four common ocular lubricants would ignite and sustain combustion in an oxygen-rich or standard room air environment.

METHODS

A model head was modified to allow placement of a cow eye and marked with 1-inch gradations from the eye. A nasal cannula supplied room air and 100% oxygen at flow rates of 0, 2, 4, and 6 L/minute. Four common ocular lubricants were chosen and placed on the eye before attempted ignition. The ignition source (an AccuTemp disposable electrocautery unit and unipolar and bipolar cautery set at 10, 20, and 30 watts) was brought down from the hairline toward the cannula. Each lubricant was tested with each ignition source and each room air/oxygen flow rate.

RESULTS

None of the ocular lubricants ignited under any of the experimental environments tested. A small surface flame was noted with the AccuTemp electrocautery unit, but it did not create a flash fire during the experiment.

CONCLUSIONS

The ocular lubricants in this experiment showed no detectable tendency to ignite, even with direct application of the ignition source. Factors such as body hair or oxygen pooling likely provided the conditions necessary for the surgical fire. Most importantly, the ophthalmic lubricants tested actually protected the corneal epithelium and decreased damage to the conjunctiva and lids.

Setup variations in locoregional radiotherapy for breast cancer: an electronic portal imaging study

Recent trials demonstrating a survival benefit with locoregional radiotherapy (LRRT) to the chest wall and regional nodes in women with node-positive breast cancer have led to increased use of complex techniques to match three or more radiation fields, but information on setup reproducibility with LRRT for breast cancer is scarce. This study reports the magnitude and directions of random and systematic deviations in LRRT for breast cancer using an offline electronic portal imaging verification protocol. Electronic portal images (EPIs) of 46 consecutive women treated with LRRT for breast cancer from March 2001 to February 2002 with LRRT were analysed. Comparisons of EPIs to the corresponding digitally reconstructed radiographs were performed offline with anatomy matching. Displacements in mm were recorded in the superior-inferior (SI), medial-lateral (ML), and anterior-posterior (AP) directions. Random errors ranged from 2.0 mm to 2.5 mm for the breast/chest wall tangential treatments and 2.3 mm to 3.9 mm for the supraclavicular nodal treatments. Systematic errors occurred to a greater degree in the AP direction for the tangential fields and in the ML direction for the supraclavicular field. Displacements of > or =10 mm were found in 1.2% of breast/chest wall tangential treatments and in 6.2% of supraclavicular nodal treatments. These data demonstrate that EPI is a useful tool to verify setup reproducibility in LRRT for breast cancer.

A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability

Although there is growing interest in finding mouse models of human disease, no technique for quickly and quantitatively determining anatomical mutants currently exists. Magnetic resonance imaging (MRI) is ideally suited to probe fine structures in mice. This technology is three-dimensional, non-destructive and rapid compared to histopathology; hence MRI scientists have been able to create detailed three-dimensional images of 60 mum resolution or better. The data is digital which lends itself to sophisticated image processing algorithms. Here we show a variational MRI atlas constructed from nine excised brains of 8 week old 129S1/SvImJ male mice. This new type of atlas is comprised of an unbiased average brain--created from alignment of the individual brains--and the mathematical descriptors of anatomical variation across the individuals. We found that the majority of internal points in the individuals never varied more than 117 microm from equivalent points in the atlas. A three-dimensional annotation of the average image was performed and used to estimate the mean and standard deviation of volumes in a variety of structures across the individual brains; these volumes never differed by more than 5%. Our results indicate that variational atlases of inbred strains represent a well-defined basis against which mutant outliers can be readily compared.

Cell–cell contact and membrane spreading in an ultrasound trap

An ultrasonic standing wave trap [Langmuir 19 (2003) 3635] in which the morphologies of 2-D latex-microparticle aggregates, forming a pressure node plane, were characterised has been applied here to different cell suspensions with increasing order of specificity of cross-linking molecule, i.e. polylysine with chondrocytes; wheat germ agglutinin (WGA) with erythrocytes and surface receptors on neural cells. The outcome of initial cell-cell contact, i.e. whether the cells stuck at the point of contact (collision efficiency = 1) or rolled around each other (collision efficiency = 0), was monitored in situ by video-microscopy. The perimeter fractal dimensions (FD) of 2-D hexagonally symmetric, closely packed aggregates of control erythrocytes and chondrocytes were 1.16 and 1.18, respectively while those for the dendrititc aggregates formed initially by erythrocytes in 0.5microg/ml WGA and chondrocytes in 20 microg/ml polylysine were 1.49 and 1.66. The FDs for control and molecularly cross-linked cells were typical of reaction-limited aggregation (RLA) and transport diffusion-limited aggregation (DLA), respectively. The FDs of the aggregates of cross-linked cells decreased with time to give more closely packed aggregates without clear hexagonal symmetry. Suspensions of neural cells formed dendritic aggregates. Spreading of inter-cellular membrane contact area occurred over 15 min for both erythrocyte and neural cell dendritic aggregates. The potential of the technique to characterise and control the progression of cell adhesion in suspension away from solid substrata is discussed.

An outbreak of hepatitis A associated with consumption of raw blueberries

This report describes the epidemiology, investigation and control of a hepatitis A (HAV) outbreak in New Zealand. Descriptive and analytical epidemiology, virology, product traceback and an orchard investigation were carried out. A case-control study revealed that 56% of 39 cases had consumed raw blueberries, compared with 14% of 71 controls (odds ratio 7.6; 95% confidence intervals 2.6-22.4). Traceback of product through retailers and wholesalers implicated a single commercial orchard. Hepatitis A virus was detected by reverse transcriptase polymerase chain reaction in faecal specimens from cases as well as a blueberry product from the orchard. Presence of hepatitis A virus was confirmed by DNA hybridization and sequencing of PCR products. Sanitary audit of the orchard revealed multiple opportunities for contamination of blueberries by pickers. This outbreak highlights the need for food safety programmes in the berry fruit industry.

Predicting the HER2 status of breast cancer from basic histopathology data: an analysis of 1500 breast cancers as part of the HER2000 International Study

The tests that are currently available for the measurement of overexpression of the human epidermal growth factor-2 (HER2) in breast cancer have shown considerable problems in accuracy and interlaboratory reproducibility. Although these problems are partly alleviated by the use of validated, standardised 'kits', there may be considerable cost involved in their use. Prior to testing it may therefore be an advantage to be able to predict from basic pathology data whether a cancer is likely to overexpress HER2. In this study, we have correlated pathology features of cancers with the frequency of HER2 overexpression assessed by immunohistochemistry (IHC) using HercepTest (Dako). In addition, fluorescence in situ hybridisation (FISH) has been used to re-test the equivocal cancers and interobserver variation in assessing HER2 overexpression has been examined by a slide circulation scheme. Of the 1536 cancers, 1144 (74.5%) did not overexpress HER2. Unequivocal overexpression (3+ by IHC) was seen in 186 cancers (12%) and an equivocal result (2+ by IHC ) was seen in 206 cancers (13%). Of the 156 IHC 3+ cancers for which complete data was available, 149 (95.5%) were ductal NST and 152 (97%) were histological grade 2 or 3. Only 1 of 124 infiltrating lobular carcinomas (0.8%) showed HER2 overexpression. None of the 49 'special types' of carcinoma showed HER2 overexpression. Re-testing by FISH of a proportion of the IHC 2+ cancers showed that only 25 (23%) of those assessable exhibited HER2 gene amplification, but 46 of the 47 IHC 3+ cancers (98%) were confirmed as showing gene amplification. Circulating slides for the assessment of HER2 score showed a moderate level of agreement between pathologists (kappa 0.4). As a result of this study we would advocate consideration of a triage approach to HER2 testing. Infiltrating lobular and special types of carcinoma may not need to be routinely tested at presentation nor may grade 1 NST carcinomas in which only 1.4% have been shown to overexpress HER2. Testing of these carcinomas may be performed when HER2 status is required to assist in therapeutic or other clinical/prognostic decision-making. The highest yield of HER2 overexpressing carcinomas is seen in the grade 3 NST subgroup in which 24% are positive by IHC.

Silence as communication in psychodynamic psychotherapy

Moments of silence in the therapy hour, on the part of the client or therapist, can communicate important psychodynamic information, as well as deeply facilitate the therapeutic encounter. The client may be communicating emotional and relational messages of need and meaning. The therapist can use silence to communicate safety, understanding and containment. However, if this intervention is not skillfully and sensitively employed by the practitioner, the client may feel the therapist's quietness as distance, disinterest, and disengagement, leading to breaches in the trust and safety of the therapeutic alliance.