A modified staining technique for arbuscular mycorrhiza compatible with molecular probes

The effects of the different steps of the root staining on the arbuscular mycorrhizal (AM) fungal rDNA extraction and amplification have been assessed. The results obtained using molecular techniques are compared with those obtained from fresh, non-stained leek roots. A modified staining procedure that eliminates heating, the use of hydrochloric acid and trypan blue, has been proved to be the most adequate to observe the AM colonisation in different plant species with/without lignified roots allowing at the same time the subsequent rDNA extraction and amplification from the stained roots. The staining technique decreased the sensitivity of the process and a higher number of roots had to be used to obtain enough material for a positive amplification. The extraction and amplification process was reliable up to 3 days after staining. A week after staining, the amplification was not dependable and after 2 weeks there was no amplification from stained material.     

A modified PAP (peroxidase-anti-peroxidase) staining technique using sera from patients with dengue hemorrhagic fever (DHF): 4 step PAP staining technique.

BHK-21 cells infected with dengue virus type 1 were stained by a newly developed 4 step PAP (peroxidase-anti-peroxidase) technique using sera from patients with dengue hemorrhagic fever as anti-virus antibody. The intensity of staining of the sera was proportional to the hemagglutination inhibition and neutralization titers. With this new technique using sera from patients it should be possible to use the PAP technique of virus infections.     

The use of monoclonal antibodies with colloidal gold-labeled probes in postembedding immunoelectron microscopy

This article focuses on procedures for the use of monoclonal antibodies (MAb) in immunoelectron microscopy (IEM) for the subcellular localization of antigens or to relate function with structure in prokaryotic and eukaryotic cells using postembedding immunoelectronmicroscopy techniques. The use of MAbs greatly increases the specificity and quality of information when used in combination with gold-labeled probes. Because of its specificity, the reactivity of MAb may be very sensitive to antigenic changes resulting from the process of sample preparation when performing IEM studies. Specific protocols for each particular combination of epitope/MAb must be usually specifically devised, since it is impossible to predict an experimental system that will successfully preserve structures and antigenic determinants for every combination. In this article, we discuss critical technical aspects that usually result in improved resolution when the procedure is used to identify structures in diverse prokaryotic, and eukaryotic cells.     

Ammoniacal silver staining of proteins: mechanism of glutaraldehyde enhancement

When the conditions for detecting proteins by ammoniacal silver staining (B. R. Oakley, D. R. Kirsch, and N. R. Morris (1980) Anal. Biochem. 105, 361-363.) following gel electrophoresis were varied, it was noted that glutaraldehyde pretreatment was necessary for maximal staining, which could not be explained simply as the result of "fixation." Further studies indicated that glutaraldehyde enhancement of protein staining with this silver reagent was probably due to oxidation of the aldehyde groups by silver ions, resulting in metallic silver depositions within the gel which act as nucleation sites for additional metallic silver localization in the protein bands upon the addition of formaldehyde developer. This proposed mechanism is consistent with the Tollen's reaction, as well as some aspects of the photographic process. Consistent with this notion, silver-staining intensities are directly related to mole percentage lysine of various standard proteins.     

Microwave irradiation improvements in the silver staining of the nucleolar organizer (Ag-NOR) technique

The well-know technique of silver staining of the nucleolar organizer (Ag-NOR) is improved in contrast, selectivity and speed when performed with microwave irradiation. The Ag-NOR technique is a very useful tool for studies on the functional morphology and molecular architecture of the nucleolus, and is reputed to be one of the best techniques for diagnosis and prognosis of cancer lesions. To test the generality of the enhancing effects. our study has involved the use of both mammalian and plant cells. Two steps in the process are improved quantitatively by microwave irradiation: fixation and staining itself. Fixation with the ethanol-based reagent, Kryofix, for 3 min in the microwave oven, resulted in good structural preservation at the optical level, and enhanced the contrast and selectivity of silver staining. On the contrary, we found that neither glutaraldehyde fixation, nor a treatment of sections with Carnoy's solution, improved Ag-NOR staining. After an analysis of the effects of the different substances involved in sample preparation, we conclude that ethanol is an essential factor for fixation for nucleolar staining, particularly if aldehydes are eliminated from fixative solutions. The process of staining was performed with a drop of staining solution on a semithin section of plastic-embedded tissue intthe microwave oven for 1 min. Staining under these conditions always improved the visualization of nucleoli, regardless of the fixation procedure. Therefore, microwave irradiation at both steps is recommended for giving the best results. Microwave irradiation probably enhances fixation by controlled heat, whereas the increase in reactivity of the staining solution is a direct effect by the microwaves on the silver ions themselves. We used this method to study nucleolar materials during mitosis in proliferating plant cells. Current applications of Ag-NOR staining can be improved with this technical modification.     

Ultracytochemistry of calmodulin binding sites in myocardial cells by staining of frozen thin sections with colloidal gold-labeled calmodulin

Calmodulin (CaM) has been implicated as a multifunctional regulator of Ca2+ in the cytoplasm of cells. We have recently introduced biologically active colloidal gold-labeled CaM as a marker for identifying potential CaM binding sites (unoccupied by endogenous CaM at the time of fixation) by electron microscopy and have stained frozen thin sections of rat cardiac muscle with this conjugate. In the presence of Ca2+, gold particles indicating CaM binding sites were found localized on the sarcoplasmic reticulum, mitochondria, and gap junctions. Control tissue sections treated with EGTA or exposed to excess amounts of unlabeled native CaM before staining showed no binding. We believe that cytochemistry of potential CaM binding sites revealed by staining with labeled exogenous CaM is useful in correlating known biochemical reactions of CaM with particular cell activities.     

Antitumor Effect of the Tyrosine Kinase Inhibitor Nilotinib on Gastrointestinal Stromal Tumor (GIST) and Imatinib-Resistant GIST Cells

Despite the benefits of imatinib for treating gastrointestinal stromal tumors (GIST), the prognosis for high risk GIST and imatinib-resistant (IR) GIST remains poor. The mechanisms of imatinib resistance have not yet been fully clarified. The aim of the study was to establish imatinib-resistant cell lines and investigate nilotinib, a second generation tyrosine kinase inhibitor (TKI), in preclinical models of GIST and imatinib-resistant GIST. For a model of imatinib-resistant GIST, we generated resistant cells from GK1C and GK3C cell lines by exposing them to imatinib for 6 months. The parent cell lines GK1C and GK3C showed imatinib sensitivity with IC₅₀ of 4.59±0.97 µM and 11.15±1.48 µM, respectively. The imatinib-resistant cell lines GK1C-IR and GK3C-IR showed imatinib resistance with IC₅₀ values of 11.74±0.17 µM (P<0.001) and 41.37±1.07 µM (P<0.001), respectively. The phosphorylation status of key cell signaling pathways, receptor tyrosine kinase KIT (CD117), platelet-derived growth factor receptor alpha (PDGFRA) and downstream signaling kinases: serine-threonine kinase Akt (AKT) and extracellular signal-regulated kinase 1/2 (ERK1/2) or the non-receptor tyrosine kinase: proto-oncogene tyrosine-protein kinase Src (SRC), was analyzed in established cell lines and ERK1/2 phosphorylation was found to be increased compared to the parental cells. Nilotinib demonstrated significant antitumor efficacy against GIST xenograft lines and imatinib-resistant GIST cell lines. Thus, nilotinib may have clinical potential for patients with GIST or imatinib-resistant GIST.     

Surgical resection for gastrointestinal stromal tumors (GIST): experience on 25 patients

Background

The benefit of pelvic lymphadenectomy in patients with cancer of the urinary bladder remains controversial. Though the inclusion of lymph node dissection in conjunction with radical cystectomy for patients with clinically negative nodes is well accepted, however, the extent of the nodal dissection remains contentious, particularly in patients with gross disease and T₁G₃ cancer. The extent of the primary bladder tumor, number of lymph nodes removed and the lymph node tumor burden are important prognostic variables in patients undergoing cystectomy. We analyzed the impact of the extent of lymphadenectomy during radical cystectomy on survival in the contemporary literature.

Methods

A Pubmed search was carried out for the literature published over the last 15 years using bladder cancer, radical cystectomy, survival, lymphadenectomy and complications as the key words. We have discussed the extent of lymphadenectomy on survival and its anatomical basis to determine the optimal number of lymph nodes to be removed and the concept of node density.

Results

Evidence from contemporary literature indicate significantly increased survival rates after cystectomy in patients with bladder cancer diagnosed with stages III or IV disease who have had relatively more lymph nodes examined, suggesting that even some patients with higher stage disease may benefit from extended pelvic lymphadenectomy at the time of cystectomy. Studies also indicate that more extensive lymphadenectomy significantly improved the prognosis of patients with bladder cancer, not only by providing prognostic information but perhaps it is also due to its inherent therapeutic value.

Conclusion

Extended lymph node dissection improves local control and survival. However, in the absence of controlled randomized trial this remains a dubitable issue.     

Gastrointestinal stromal tumors (GIST): Facing cell death between autophagy and apoptosis

Autophagy and apoptosis are 2 fundamental biological mechanisms that may cooperate or be antagonistic, although both are involved in deciding the fate of cells in physiological or pathological conditions. These 2 mechanisms coexist simultaneously in cells and share common upstream signals and stimuli. Autophagy and apoptosis play pivotal roles in cancer development. Autophagy plays a key function in maintaining tumor cell survival by providing energy during unfavorable metabolic conditions through its recycling mechanism, and supporting the high energy requirement for metabolism and growth. This review focuses on gastrointestinal stromal tumors and cell death through autophagy and apoptosis, taking into account the involvement of both of these processes in tumor development and growth and as mechanisms of drug resistance. We also focus on the crosstalk between autophagy and apoptosis as an emerging field with major implications for the development of novel therapeutic options.     

microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets.     

Mouse linkage cytogenetics (L-C) probes

We have identified 149 hybridization probes at 10-cM intervals in the mouse and have confirmed their order and linkage by fluorescence in situ hybridization. These probes represent a new resource for mapping in the mouse and can be used to correlate linkage and cytogenetic maps, to map novel sequences to within a few centimorgans, to relate cytogenetic abnormalities to the genetic map, and to make cross-species comparisons.     

Silver enhancement of protein A-gold probes on resin-embedded ultrathin sections

Summary A simple method is described allowing the enhancement of the visibility of small gold probes for the electron microscopy.This method, which allows the silver intensification of gold directly on epon-embedded ultrathin sections, was used for the electron microscopic localization of Mouse Mammary Tumor Virus (MMTV) antigens in cultured cells derived from GR and BALB/cfRIII mouse mammary tumors. After the immunostaining with the preembedding protein A-gold technique, the ultrathin sections, placed on 200 mesh copper grids, were rehydrated and exposed to a photographic developer containing silver nitrate. During this physical development gold particles are incapsulated in growing shells of metallic silver, which gradually become more and more visible. We were able to obtain a heavy labelling of the viral particles, well visible even at low magmfication, with a negligeable background staining.The present technique can be useful whenever it is necessary to use the smallest gold probes today available.Supported by contract No. 85.02038.44 from the National Research Council, Rome, Progetto Finalizzato Oncologia     

Improved avidin-biotin-peroxidase complex (ABC) staining

Summary A considerable intensification of the avidin—biotin—peroxidase complex staining system (ABC) was obtained by sequentially overlaying the sections to be immunostained with an avidin-rich and a biotin-rich complex. Each sequential addition contributed to the deposition of horseradish peroxidase on the immunostained site and allowed the subsequent binding of a complementary complex. With this technique a higher dilution of the antisera could be used and minute amounts of antigen masked by the fixative could be demonstrated on paraffin sections.     

Recent advances and novel agents for gastrointestinal stromal tumor (GIST)

Contemporary advancements have had little impact on the treatment of gastric cancer (GC), the world??s second highest cause of cancer death. Agents targeting human epidermal growth factor receptor mediated pathways have been a common topic of contemporary cancer research, including monoclonal antibodies (mAbs) and receptor tyrosine kinase inhibitors (TKIs). Trastuzumab is the first target agent evidencing improvements in overall survival in HER2-positive (human epidermal growth factor receptor 2) gastric cancer patients. Agents targeting vascular epithelial growth factor (VEGF), mammalian target of rapamycin (mTOR), and other biological pathways are also undergoing clinical trials, with some marginally positive results. Effective targeted therapy requires patient selection based on predictive molecular biomarkers. Most phase III clinical trials are carried out without patient selection; therefore, it is hard to achieve personalized treatment and to monitor patient outcome individually. The trend for future clinical trials requires patient selection methods based on current understanding of GC biology with the application of biomarkers.     

Tris (phenanthroline) metal complexes: probes for DNA helicity

The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of helical unwinding, optical enrichment studies by equilibrium dialysis and luminescence titrations with separated enantiomers of (phen)3Ru2+ all indicate that the delta isomer binds preferentially to the right-handed duplex. The chiral discrimination is governed by the DNA helical asymmetry. Complete stereospecifity is seen with isomers of the bulkier RuDIP (tris-4,7-diphenylphenanthrolineruthenium(II]. While both isomers bind to Z-DNA, a poor template for discrimination, binding of lambda-RuDIP to B-DNA is precluded. These chiral complexes therefore serve as a chemical probe to distinguish left and right-handed DNA helices in solution.     

Sandwich hybridization probes for the detection of Pseudo-nitzschia (Bacillariophyceae) species: An update to existing probes and a description of new probes

New sandwich hybridization assay (SHA) probes for detecting Pseudo-nitzschia species (P. arenysensis, P. fraudulenta, P. hasleana, P. pungens) are presented, along with updated cross-reactivity information on historical probes (SHA and FISH; fluorescence in situ hybridization) targeting P. australis and P. multiseries. Pseudo-nitzschia species are a cosmopolitan group of diatoms that produce varying levels of domoic acid (DA), a neurotoxin that can accumulate in finfish and shellfish and transfer throughout the food web. Consumption of infected food sources can lead to illness in humans (amnesic shellfish poisoning; ASP) and marine wildlife (domoic acid poisoning; DAP). The threat of human illness, along with economic loss from fishery closures has resulted in the implementation of monitoring protocols and intensive ecological studies. SHA probes have been instrumental in some of these efforts, as the technique performs well in complex heterogeneous sample matrices and has been adapted to benchtop and deployable (Environmental Sample Processor) platforms. The expanded probe set will enhance future efforts towards understanding spatial, temporal and successional patterns in species during bloom and non-bloom periods.