Basic confocal microscopy

Confocal microscopy produces sharp images of structures within relatively thick specimens (up to several hundred microns). It is particularly useful for examining fluorescent specimens. This overview intended to provide background and practical tips needed to get started with confocal microscopy. It begins with a description of the basis of optical sectioning, then discusses various types of confocal microscopes, and concludes with practical guidelines for sample preparation and optimizing image acquisition parameters.

Serous carcinoma of the uterus-determination of HER-2/neu status using immunohistochemistry, chromogenic in situ hybridization, and quantitative polymerase chain reaction techniques: its significance and clinical correlation

Uterine serous papillary carcinoma (USPC) are high-grade tumors with Her2 gene expression and poor prognosis. The human gene Her2 is a proto-oncogene that encodes a protein with tyrosine kinase activity. The objective of this study was to determine Her2 protein expression and gene amplification in USPC using three methods: immunohistochemistry (IHC), chromogenic in situ hybridization (CISH), and quantitative polymerase chain reaction (Q-PCR), to compare the three techniques, and to correlate Her2 expression and amplification with clinical outcome. Clinical data were obtained from the records of the patients provided by the database of the Gynaecological Cancer Unit at the Royal Adelaide Hospital. Paraffin-embedded tissues of 45 cases were examined using three techniques. Her2 positive rate was 40%. About 13% was strongly positive by all three methods. About 67% Her2 positive patients had advanced-stage disease. Relapse rate was 61% (P = 0.6). Stages I and II had a better survival with negative receptor. Age and stage were major prognostic variables in Cox analysis. Marker status did not reach statistical significance in overall survival (OS) and relapse-free survival (RFS), but had a hazard ratio (HR) of 1.5 in RFS. Five-year OS with Her2 negative was 39%. HR was 0.97 (95% CI 0.46-2.1). RFS was 39% and HR was 1.4 (95% CI 0.65-2.9). The three methods have strong correlation. IHC, 3+ positive cases should be regarded as exhibiting evidence of gene amplification and do not require further testing. Equivocal results require further testing by CISH or PCR. Age and stage are strong prognostic variables and receptor status has a HR of 1.5 in RFS. The therapeutic role of Trastuzumab should be tested in clinical trial setting.

Basic confocal microscopy

This comprehensive overview unit introduces the reader to confocal microscopy from the basic principles of imaging and optical sectioning, to selection of laser, practical guidelines for fixation, choice of fluorophore, control samples, and mounting the sample. There are also suggestions for optimizing the imaging parameters.

Treatment of a metallic foreign body in the cranial cervical region of a horse

Ingestion of foreign bodies is uncommon in horses when compared with indiscriminate grazers such as cattle. This case report describes the diagnosis and treatment of a cervical abscess in a Thoroughbred racehorse thought to be associated with ingestion of wire. Radiographic and ultrasonographic examination provided a diagnosis, and conservative treatment of the lesion with antimicrobials initially allowed the lesion to localise closer to the skin for safer surgical exploration. Intra-operative ultrasonographic imaging facilitated surgical access, removal of the foreign body, and drainage. While surgical treatment is usually necessary to resolve an abscess, initially conservative therapy may help to improve the prognosis by simplifying surgical access and reducing the risk of surgical complications.

Decision making during nuclear power plant incidents: a new approach to the evaluation of precursor events

Renewed interest in precursor analysis has shown that the evaluation of near misses is an interdisciplinary effort, fundamental within the life of an organization for reducing operational risks and enabling accident prevention. The practice of precursor analysis has been a part of nuclear power plant regulation in the United States for over 25 years. During this time, the models used in the analysis have evolved from simple risk equations to quite complex probabilistic risk assessments. But, one item that has remained constant over this time is that the focus of the analysis has been on modeling the scenario using the risk model (regardless of the model sophistication) and then using the results of the model to determine the severity of the precursor incident. We believe that evaluating precursors in this fashion could be a shortcoming since decision making during the incident is not formally investigated. Consequently, we present the idea for an evaluation procedure that enables one to integrate current practice with the evaluation of decisions made during the precursor event. The methodology borrows from technologies both in the risk analysis and the decision analysis realms. We demonstrate this new methodology via an evaluation of a U.S. precursor incident. Specifically, the course of the incident is represented by the integration of a probabilistic risk assessment model (i.e., the risk analysis tool) with an influence diagram and the corresponding decision tree (i.e., the decision analysis tools). The results and insights from the application of this new methodology are discussed.

Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes

Acetylation of histone H3 on lysine 56 occurs during mitotic and meiotic S phase in fungal species. This acetylation blocks a direct electrostatic interaction between histone H3 and nucleosomal DNA, and the absence of this modification is associated with extreme sensitivity to genotoxic agents. We show here that H3-K56 acetylation is catalyzed when Rtt109, a protein that lacks significant homology to known acetyltransferases, forms an active complex with either of two histone binding proteins, Asf1 or Vps75. Rtt109 binds to both these cofactors, but not to histones alone, forming enzyme complexes with kinetic parameters similar to those of known histone acetyltransferase (HAT) enzymes. Therefore, H3-K56 acetylation is catalyzed by a previously unknown mechanism that requires a complex of two proteins: Rtt109 and a histone chaperone. Additionally, these complexes are functionally distinct, with the Rtt109/Asf1 complex, but not the Rtt109/Vps75 complex, being critical for resistance to genotoxic agents.

DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC

ATP-dependent chromatin-remodeling complexes (remodelers) modulate gene transcription by regulating the accessibility of highly packaged genomic DNA. However, the molecular mechanisms involved at the nucleosomal level in this process remain controversial. Here, we monitor the real-time activity of single ySWI/SNF or RSC complexes on single, stretched nucleosomal templates under tensions above 1 pN forces. We find that these remodelers can translocate along DNA at rates of approximately 13 bp/s and generate forces up to approximately 12 pN, producing DNA loops of a broad range of sizes (20-1200 bp, average approximately 100 bp) in a nucleosome-dependent manner. This nucleosome-specific activity differs significantly from that on bare DNA observed under low tensions and suggests a nucleosome-remodeling mechanism through intranucleosomal DNA loop formation. Such loop formation may provide a molecular basis for the biological functions of remodelers.

Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules

Chromatin-remodeling enzymes can overcome strong histone-DNA interactions within the nucleosome to regulate access of DNA-binding factors to the genetic code. By unzipping individual DNA duplexes, each containing a uniquely positioned nucleosome flanked by long segments of DNA, we directly probed histone-DNA interactions. The resulting disruption-force signatures were characteristic of the types and locations of interactions and allowed measurement of the positions of nucleosomes with 2.6-base-pair (bp) precision. Nucleosomes remodeled by yeast SWI/SNF were moved bidirectionally along the DNA, resulting in a continuous position distribution. The characteristic distance of motion was approximately 28 bp per remodeling event, and each event occurred with a catalytic efficiency of 0.4 min(-1) per nM SWI/SNF. Remodeled nucleosomes had essentially identical disruption signatures to those of unremodeled nucleosomes, indicating that their overall structure remained canonical. These results impose substantial constraints on the mechanism of SWI/SNF remodeling.

Recent advances in equine abdominal surgery

Laparoscopy is a minimally invasive procedure that has applications as a diagnostic, therapeutic and prognostic technique. Specialized equipment is necessary to perform equine laparoscopy, and there is a large range of instruments, both disposable and non-disposable available. Laparoscopic procedures described include ovariectomy, cryptorchidectomy, adhesiolysis and herniorrhaphy. Laparoscopy can be performed in a standing or dorsally recumbent position, depending on surgeon preference, patient status and the procedure to be performed. Stapling equipment is frequently used in gastrointestinal surgery in horses. Advantages include decreased surgical time and a decrease in the risk of contamination. Stapling equipment is often used in creating anastomoses, both in the large and small intestines, as well as in vessel ligation. New surgical techniques intended to decrease adhesion formation include the use of carboxymethylcellulose and bioresorbable patches. Indwelling abdominal drains can be used for peritoneal lavage following surgery and also appear to decrease the risk of adhesion formation. Improvements in post-operative care, including the treatment of post-operative ileus and endotoxaemia can significantly improve the outcome of horses that have undergone surgery for abdominal disorders. Recommendations for the use of prokinetic agents in horses with ileus vary widely. Prokinetic agents include local anaesthetics, macrolide antimicrobials, cholinergic agonists and dopamine antagonists. Endotoxaemia is common in horses following surgery for gastrointestinal disorders. The antibiotic polymyxin B binds to the circulating endotoxin molecule, decreasing its half-life in the intra-vascular space and reducing associated inflammation. This drug appears to be an effective and affordable treatment option for horses with endotoxaemia. The use of specific cyclooxygenase inhibitors in veterinary medicine have been studied recently. Selective cyclooxygenase-2 inhibitors may provide comparable anti-inflammatory and analgesic properties to the non-selective non-steroidal anti-inflammatory drugs. These drugs appear to have similar clinical effectiveness and will hopefully minimize deleterious side effects. The optimal healing of ventral midline incisions in horses is related to many factors including appropriate suture patterns and bite size, in addition to appropriate post-operative exercise recommendations. Recent advances in surgical techniques and post-operative care should decrease the morbidity and mortality associated with abdominal surgery. This article provides an overview of some of these advances.

A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling

Yeast (Saccharomyces cerevisiae) SWI/SNF is a prototype for a large family of ATP-dependent chromatin-remodeling enzymes that facilitate numerous DNA-mediated processes. Swi2/Snf2 is the catalytic subunit of SWI/SNF, and it is the founding member of a novel subfamily of the SF2 superfamily of DNA helicase/ATPases. Here we present a functional analysis of the diagnostic set of helicase/ATPase sequence motifs found within all Swi2p/Snf2p family members. Whereas many of these motifs play key roles in ATP binding and/or hydrolysis, we identify residues within conserved motif V that are specifically required to couple ATP hydrolysis to chromatin-remodeling activity. Interestingly, motif V of the human Swi2p/Snf2p homolog, Brg1p, has been shown to be a possible hot spot for mutational alterations associated with cancers.

The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

DNA instructed displacement of histones H2A and H2B at an inducible promoter

Regulation of gene expression requires dynamic changes in chromatin, but the nature of these changes is not well understood. Here, we show that progesterone treatment of cultured cells leads to recruitment of progesterone receptor (PR) and SWI/SNF-related complexes to Mouse Mammary Tumor Virus (MMTV) promoter, accompanied by displacement of histones H2A and H2B from the nucleosome containing the receptor binding sites, but not from adjacent nucleosomes. PR recruits SWI/SNF to MMTV nucleosomes in vitro and facilitates synergistic binding of receptors and nuclear factor 1 to the promoter. In nucleosomes assembled on MMTV or mouse rDNA promoter sequences, SWI/SNF catalyzes ATP-dependent sliding of the histone octamer followed only on the MMTV promoter by displacement of histones H2A and H2B. In MMTV nucleosome arrays, SWI/SNF displaces H2A and H2B from nucleosome B and not from the adjacent nucleosome. Thus, the outcome of nucleosome remodeling by SWI/SNF depends on DNA sequence.

Positron emission tomography scanning in the assessment of patients with lymphoma

BACKGROUND

The detection of lymphoma by computed tomography (CT) scanning is known to be improved by positron emission tomography (PET) and/or gallium scanning, although the direct comparative accuracy of these imaging modalities remains a subject of ongoing review.

AIMS

The aim of the present study was to compare PET scanning with conventional imaging (CT and/or gallium scanning) in patients with lymphoma.

METHODS

A retrospective study of 38 patients (25 men; 13 women; median age 39.5 years; range 18.0-81.0 years) who had had PET scans (24 scans at initial staging and 46 scans at restaging, including suspected disease relapse) was carried out. Thirty-one concurrent gallium scans had been performed. Disease was validated with clinical follow up or biopsy.

RESULTS

The sensitivities of PET and CT at initial staging were 96 and 71%, respectively. PET identified additional sites of disease compared with CT in 29% of patients. Of the 15 patients who had had all three imaging modalities, the sensitivities of PET, CT and gallium were 93, 67 and 87%, respectively. At treatment completion, the positive predictive values of PET, CT and gallium scans for relapse given a residual mass were 100, 33 and 0%, respectively (P = 0.006 for PET and CT comparison). The negative predictive values of PET, CT and gallium were 76, 0 and 70%, respectively (P-value not significant). In suspected disease relapse, PET results changed management in 50% of patients.

CONCLUSION

Compared with CT and gallium scans, PET has superior accuracy in staging and restaging, and its greatest value lies in its positive predictive value for relapse in patients with residual masses.

Estrogen receptor-alpha interaction with the CREB binding protein coactivator is regulated by the cellular environment

The p160 coactivators, steroid receptor coactivator-1 (SRC-1), transcriptional intermediary factor-2 (TIF2) and receptor-associated coactivator-3 (RAC3), as well as the coactivator/integrator CBP, mediate estrogen receptor-alpha (ERalpha)-dependent gene expression. Although these coactivators are widely expressed, ERalpha transcriptional activity is cell-type dependent. In this study, we investigated ERalpha interaction with p160 coactivators and CBP in HeLa and HepG2 cell lines. Basal and estradiol (E2)-dependent interactions between the ERalpha ligand-binding domain (LBD) and SRC-1, TIF2 or RAC3 were observed in HeLa and HepG2 cells. The extents of hormone-dependent interactions were similar and interactions between each of the p160 coactivators and the ERalpha LBD were not enhanced by 4-hydroxytamoxifen in either cell type. In contrast to the situation for p160 coactivators, E2-dependent interaction of the ERalpha LBD with CBP or p300 was detected in HeLa but not HepG2 cells by mammalian two-hybrid and coimmunoprecipitation assays, indicating that the cellular environment modulates ERalpha-CBP/p300 interaction. Furthermore, interactions between CBP and p160 coactivators are much more robust in HeLa than HepG2 cells suggesting that poor CBP-p160 interactions are insufficient to support ERalpha-CBP-p160 ternary complexes important for nuclear receptor-CBP interactions. Alterations in p160 coactivators or CBP expression between these two cell types did not account for differences in ERalpha-p160-CBP interactions. Taken together, these data revealed the influence of cellular environment on ERalpha-CBP/p300 interactions, as well as CBP-p160 coactivator binding, and suggest that these differences may contribute to the cell specificity of ERalpha-dependent gene expression.

The Mouse Genome Database (MGD): integrating biology with the genome

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

ATP-dependent chromatin remodeling

The study of chromatin and how this dynamic structure modulates events in the eukaryotic nucleus has become an increasingly important topic in biomedical research. A large number of enzymes have been discovered that are responsible for modifying and altering chromatin structure, either globally or specifically at particular gene promoters or regions of the chromosome. This chapter provides an introduction to the structure of chromatin and then describes how special classes of enzymes modulate chromatin structure to allow access to DNA.

Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexes

Rapid protein purification methodologies, such as strategies involving the tandem affinity purification module, have resulted in the identification of a tremendous number of multisubunit protein complexes. Furthermore, in this modern genomic age, mass spectrometry methods are often coupled with affinity purification to identify the genes that encode each protein subunit. However, simple methodologies to determine the stoichiometry of individual subunits within a multisubunit complex have not received much attention. In this article we describe a procedure to rapidly and efficiently determine the stoichiometry of subunits within multisubunit complexes using a combination of tandem affinity purification and quantitative 125I labeling of subunit tyrosines.

Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase

Nucleosomes inhibit DNA repair in vitro, suggesting that chromatin remodeling activities might be required for efficient repair in vivo. To investigate how structural and dynamic properties of nucleosomes affect damage recognition and processing, we investigated repair of UV lesions by photolyase on a nucleosome positioned at one end of a 226-bp-long DNA fragment. Repair was slow in the nucleosome but efficient outside. No disruption or movement of the nucleosome was observed after UV irradiation and during repair. However, incubation with the nucleosome remodeling complex SWI/SNF and ATP altered the conformation of nucleosomal DNA as judged by UV photo-footprinting and promoted more homogeneous repair. Incubation with yISW2 and ATP moved the nucleosome to a more central position, thereby altering the repair pattern. This is the first demonstration that two different chromatin remodeling complexes can act on UV-damaged nucleosomes and modulate repair. Similar activities might relieve the inhibitory effect of nucleosomes on DNA repair processes in living cells.

Structural analysis of the yeast SWI/SNF chromatin remodeling complex

Elucidating the mechanism of ATP-dependent chromatin remodeling is one of the largest challenges in the field of gene regulation. One of the missing pieces in understanding this process is detailed structural information on the enzymes that catalyze the remodeling reactions. Here we use a combination of subunit radio-iodination and scanning transmission electron microscopy to determine the subunit stoichiometry and native molecular weight of the yeast SWI/SNF complex. We also report a three-dimensional reconstruction of yeast SWI/SNF derived from electron micrographs.

Vector-averaged gravity-induced changes in cell signaling and vitamin D receptor activity in MG-63 cells are reversed by a 1,25-(OH)2D3 analog, EB1089

Skeletal unloading in an animal hindlimb suspension model and microgravity experienced by astronauts or as a result of prolonged bed rest causes site-specific losses in bone mineral density of 1%-2% per month. This is accompanied by reductions in circulating levels of 1,25-(OH)(2)D(3), the active metabolite of vitamin D. 1,25-(OH)(2)D(3), the ligand for the vitamin D receptor (VDR), is important for calcium absorption and plays a role in differentiation of osteoblasts and osteoclasts. To examine the responses of cells to activators of the VDR in a simulated microgravity environment, we used slow-turning lateral vessels (STLVs) in a rotating cell culture system. We found that, similar to cells grown in microgravity, MG-63 cells grown in the STLVs produce less osteocalcin, alkaline phosphatase, and collagen Ialpha1 mRNA and are less responsive to 1,25-(OH)(2)D(3). In addition, expression of VDR was reduced. Moreover, growth in the STLV caused activation of the stress-activated protein kinase pathway (SAPK), a kinase that inhibits VDR activity. In contrast, the 1,25-(OH)(2)D(3) analog, EB1089, was able to compensate for some of the STLV-associated responses by reducing SAPK activity, elevating VDR levels, and increasing expression of osteocalcin and alkaline phosphatase. These studies suggest that, not only does simulated microgravity reduce differentiation of MG-63 cells, but the activity of the VDR, an important regulator of bone metabolism, is reduced. Use of potent, less calcemic analogs of 1,25-(OH)(2)D(3) may aid in overcoming this defect.