Analysis of 3D elemental mapping artefacts in biological specimens using Monte Carlo simulation

In this paper, we present Monte Carlo simulation results demonstrating the feasibility of using the focused ion beam based X-ray microanalysis technique (FIB-EDS) for the 3D elemental analysis of biological samples. In this study, we used a marine diatom Thalassiosira pseudonana as our model organism and NISTMonte for the Monte Carlo simulations. We explored several beam energies commonly used for the X-ray microanalysis to examine their effects on the resulting 3D elemental volume of the model organism. We also performed a preliminary study on the sensitivity of X-ray analysis for detecting nanoparticles in the model. For the conditions considered in this work, we show that the X-ray mapping performed using the 5 keV beam energy results in 3D elemental distributions that closely reflect the elemental distributions in the original model. At 5 keV, the depth resolution of the X-ray maps is about 250 nm for the model organism. We also show that the nanoparticles that are 50 nm in diameter or greater are easily located. Although much work is still needed in generating more accurate biological models and simulating experimental conditions relevant to these samples, our results indicate that FIB-EDS is a promising technique for the 3D elemental analysis of some biological specimens.

Crystallization and preliminary X-ray analysis of the human respiratory syncytial virus nucleocapsid protein

Human respiratory syncytial virus (HRSV) has a nonsegmented negative-stranded RNA genome which is encapsidated by the HRSV nucleocapsid protein (HRSVN) that is essential for viral replication. HRSV is a common cause of respiratory infection in infants, yet no effective antiviral drugs to combat it are available. Recent data from an experimental anti-HRSV compound, RSV-604, indicate that HRSVN could be the target site for drug action. Here, the expression, purification and preliminary data collection of decameric HRSVN as well as monomeric N-terminally truncated HRSVN mutants are reported. Two different crystal forms of full-length selenomethionine-labelled HRSVN were obtained that diffracted to 3.6 and approximately 5 A resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 133.6, b = 149.9, c = 255.1 A, and space group P2(1), with unit-cell parameters a = 175.1, b = 162.6, c = 242.8 A, beta = 90.1 degrees , respectively. For unlabelled HRSVN, only crystals belonging to space group P2(1) were obtained that diffracted to 3.6 A. A self-rotation function using data from the orthorhombic crystal form confirmed the presence of tenfold noncrystallographic symmetry, which is in agreement with a reported electron-microscopic reconstruction of HRSVN. Monomeric HRSVN generated by N-terminal truncation was designed to assist in structure determination by reducing the size of the asymmetric unit. Whilst such HRSVN mutants were monomeric in solution and crystallized in a different space group, the size of the asymmetric unit was not reduced.

Inflammatory tumour cell killing by oncolytic reovirus for the treatment of melanoma

Reovirus is a promising unmodified double-stranded RNA (dsRNA) anti-cancer oncolytic virus, which is thought to specifically target cells with activated Ras. Although reovirus has been tested in a wide range of preclinical models and has entered early clinical trials, it has not previously been tested for the treatment of human melanoma. Here, we show that reovirus effectively kills and replicates in both human melanoma cell lines and freshly resected tumour; intratumoural injection also causes regression of melanoma in a xenograft in vivo model. Reovirus-induced melanoma death is blocked by caspase inhibition and is dependent on constituents of the Ras/RalGEF/p38 pathway. Reovirus melanoma killing is more potent than, and distinct from, chemotherapy or radiotherapy-induced cell death; a range of inflammatory cytokines and chemokines are released by infected tumour cells, while IL-10 secretion is abrogated. Furthermore, the inflammatory response generated by reovirus-infected tumour cells causes bystander toxicity against reovirus-resistant tumour cells and activates human myeloid dendritic cells (DC) in vitro. Hence, reovirus is suitable for clinical testing in melanoma, and may provide a useful danger signal to reverse the immunologically suppressive environment characteristic of this tumour.

Elevated B6 levels and peripheral neuropathies

Polyneuropathy related to decreased levels of Vitamin B6 are well known. In contrast, the association between elevated levels of pyridoxine and neuropathy is not well described. This study is a retrospective review of patients in our neuromuscular clinic that were found to have elevated B6 levels. Twenty-six patients were found to have elevated serum B6 levels. The mean B6 level was 68.8 ng/ml. Twenty patients (76.9%) reported daily vitamin use. Twenty-one patients (80.8%) reported only sensory complaints. The most common symptoms reported were numbness (96%), burning pain (49.9%), tingling (57.7%), balance difficulties (30.7%), and weakness (7.8%). Nine (out of 26) had an abnormal EMG/NCS. Eight patients had an abnormal quantitative sensory study. We conclude that elevated pyridoxine levels should be considered in the differential diagnosis of any sensory or sensorimotor polyneuropathy.

False positive rate of thoracic outlet syndrome diagnostic maneuvers

OBJECTIVE

In this study, we aim to determine the false-positive rate & specificity in normal subjects and carpal tunnel syndrome (CTS) patients of five provocative maneuvers used to diagnose thoracic outlet syndrome (TOS).

DESIGN/METHODS

We prospectively evaluated subjects with clinical and electrophysiological evidence of CTS as well as normal subjects. All subjects underwent provocative testing by a blinded physician, which included the Adson A & B tests, Costoclavicular maneuver (CCM), Elevated arm stress test (Roos), and Supraclavicular pressure (SCP).

RESULTS

In the CTS group, false positive tests were observed in 42% in the Adson A test, 45% in the Adson B test, 48% in the CCM, 77% in the Roos test, and 61% in the SCP 94% of the CTS patients had at least 1 positive TOS diagnostic maneuver. In the normal group, false positive tests were observed in 9% in the Adson A test, 20% in the Adson B test, 16% in the CCM, 47% in the Roos test, and 30% in the SCP 56% of the normal patients had at least 1 positive TOS diagnostic maneuver.

CONCLUSIONS

We conclude that current provocative maneuvers used to diagnose TOS result in a high false-positive rate in normal subjects and an even higher false-positive rate in CTS patients.

Effects of timolol on MYOC, OPTN, and WDR36 RNA levels

OBJECTIVES

To evaluate if timolol affects expression of 3 open-angle glaucoma genes and to study its ability to modulate dexamethasone-induced up-regulation of MYOC.

METHODS

We used quantitative polymerase chain reaction assay of glaucoma gene transcript levels from human trabecular meshwork (HTM) cultures exposed to 3 different doses of timolol. Three HTM cell cultures were grown with or without 1 of 3 timolol doses in the presence or absence of dexamethasone.

RESULTS

All 3 concentrations of timolol reduced MYOC RNA levels in 1 HTM culture compared with an untreated control and showed negligible effects in the other 2 cultures. Timolol had no effect on dexamethasone-induced MYOC transcript levels in any of the 3 cultures. Timolol, dexamethasone, and dexamethasone plus timolol had a negligible effect on OPTN and WDR36 RNA levels.

CONCLUSIONS

Timolol can reduce MYOC RNA levels in HTM cultures from some individuals. Timolol does not alter OPTN or WDR36 levels or ameliorate MYOC induction by dexamethasone in vitro.

CLINICAL RELEVANCE

It remains to be determined whether timolol could reduce production of misfolded myocilin protein by HTM cells in individuals with MYOC missense mutations. A broader survey of interindividual variation in response to timolol as well as mechanistic studies are still needed before potential therapeutic implications can be explored.

Mathematical model for microbial fuel cells with anodic biofilms and anaerobic digestion

This study describes the integration of IWA's anaerobic digestion model (ADM1) within a computational model of microbial fuel cells (MFCs). Several populations of methanogenic and electroactive microorganisms coexist suspended in the anolyte and in the biofilm attached to the anode. A number of biological, chemical and electrochemical reactions occur in the bulk liquid, in the biofilm and at the electrode surface, involving glucose, organic acids, H2 and redox mediators. Model output includes the evolution in time of important measurable MFC parameters (current production, consumption of substrates, suspended and attached biomass growth). Two- and three-dimensional model simulations reveal the importance of current and biomass heterogeneous distribution over the planar anode surface. Voltage- and power-current characteristics can be calculated at different moments in time to evaluate the limiting regime in which the MFC operates. Finally, model simulations are compared with experimental results showing that, in a batch MFC, smaller electrical resistance of the circuit leads to selection of electroactive bacteria. Higher coulombic yields are so obtained because electrons from substrate are transferred to anode rather than following the methanogenesis pathway. In addition to higher currents, faster COD consumption rates are so achieved. The potential of this general modelling framework is in the understanding and design of more complex cases of wastewater-fed microbial fuel cells.

Polymorphic MLH1 and risk of cancer after methylating chemotherapy for Hodgkin lymphoma

BACKGROUND AND OBJECTIVE

Methylating agents are effective chemotherapy agents for Hodgkin lymphoma, but are associated with the development of second primary cancers. Cytotoxicity of methylating agents is mediated primarily by the DNA mismatch repair (MMR) system. Loss of MLH1, a major component of DNA MMR, results in tolerance to the cytotoxic effects of methylating agents and persistence of mutagenised cells at high risk of malignant transformation. We hypothesised that a common substitution in the basal promoter of MLH1 (position -93, rs1800734) modifies the risk of cancer after methylating chemotherapy.

METHODS

133 patients who developed cancer following chemotherapy and/or radiotherapy (n = 133), 420 patients diagnosed with de novo myeloid leukaemia, 242 patients diagnosed with primary Hodgkin lymphoma, and 1177 healthy controls were genotyped for the MLH1 -93 polymorphism by allelic discrimination polymerase chain reaction (PCR) and restriction fragment length polymorphism assay. Odds ratios and 95% confidence intervals for cancer risk by MLH1 -93 polymorphism status, and stratified by previous exposure to methylating chemotherapy, were calculated using unconditional logistic regression.

RESULTS

Carrier frequency of the MLH1 -93 variant was higher in patients who developed therapy related acute myeloid leukaemia (t-AML) (75.0%, n = 12) or breast cancer (53.3%. n = 15) after methylating chemotherapy for Hodgkin lymphoma compared to patients without previous methylating exposure (t-AML, 30.4%, n = 69; breast cancer patients, 27.2%, n = 22). The MLH1 -93 variant allele was also over-represented in t-AML cases when compared to de novo AML cases (36.9%, n = 420) and healthy controls (36.3%, n = 952), and was associated with a significantly increased risk of developing t-AML (odds ratio 5.31, 95% confidence interval 1.40 to 20.15), but only in patients previously treated with a methylating agent.

CONCLUSIONS

These data support the hypothesis that the common polymorphism at position -93 in the core promoter of MLH1 defines a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma. However, replication of this finding in larger studies is suggested.

Image-guided pleural biopsy: diagnostic yield and complications

BACKGROUND

Pleural biopsy and cytology are standard procedures for the investigation of pleural disease. Recent medical literature has suggested that image-guided pleural biopsy shows improved sensitivity for the diagnosis of pleural malignancy, when compared with the more commonly performed reverse bevel needle biopsy such as Abrams' needle. In our centre there has been an increasing trend towards performing image-guided pleural biopsies, and to our knowledge there is no large published series documenting the complication rate and diagnostic yield.

METHODS

The radiology and pathology databases were searched for all image-guided [computed tomography (CT) and ultrasound (US)] pleural biopsies from January 2001 to December 2004. All imaging and histology were reviewed, and final diagnostic information about patients was obtained from the respiratory multidisciplinary team database and patient notes. A record was made of complications following biopsy, presence of pleura in the biopsy, and adequacy of tissue for histological diagnosis.

RESULTS

A total of 82 patients underwent 85 image-guided pleural biopsies over a 4-year period. 80 cases were performed under CT and five under US guidance. The rate of new pneumothorax detected by chest radiography was 4.7%. No patient required a chest drain or blood transfusion to treat complications. In 10 (12%) cases, there was inadequate tissue to reach a confident histological diagnosis and in eight (9%) of these, no pleura was present. Assuming all suspicious and inadequate biopsies are treated as benign, which is the worst case scenario, image-guided pleural biopsy has a sensitivity and specificity of 76% and 100%, respectively, for the diagnosis of malignant disease.

CONCLUSIONS

Image-guided pleural biopsy is a safe procedure with few associated complications and has a higher sensitivity than previously published series for reverse cutting needle biopsy in the diagnosis of malignant pleural disease.

Aspirin-treated human DCs up-regulate ILT-3 and induce hyporesponsiveness and regulatory activity in responder T cells

Mature dendritic cells (mDCs) are potent antigen presenting cells, but immature DCs (iDCs) have been shown to have reduced antigen stimulatory capacity. Different strategies have been investigated to augment the tolerogenic capacity of dendritic cells (DCs). We demonstrate that in aspirin-treated human DCs, there is reduced expression of CD1a, HLA-DR and CD86, up-regulation of ILT-3 expression and marginal increases in PDL-1. Aspirin-treated DCs are partially resistant to phenotypic changes following maturational stimuli, such as lipopolysaccharide (LPS) or TNFalpha, IL-1alpha and PGE2. Aspirin-treated DCs demonstrate normal endocytic function, but have a reduced ability to stimulate allogeneic T cells, which is comparable to iDCs. Furthermore, they induce hyporesponsiveness and regulatory activity in responder naïve and memory T cells; for naïve T cells this is achieved more quickly and efficiently than with iDCs. We investigated the mechanism of this regulatory activity and found that both cell-cell contact and inhibitory cytokine activity are involved, although no one cytokine predominates in importance. Blocking ILT-3 or IL-12 does not diminish the capacity of these DCs to induce regulation or Foxp3 expression on the regulatory T cells. Results demonstrate that aspirin-treated DCs display tolerogenic potential, which is of interest in their therapeutic potential in reducing chronic allograft rejection.

Surgical debridement of craniocervical necrotizing fasciitis: the window of opportunity

Craniocervical necrotizing fasciitis (CCNF) has a potentially high morbidity and mortality. Late presentation, shock and disseminated intravascular coagulation are associated with a particularly poor prognosis. Early recognition and aggressive treatment is advised. A case report is presented of a late presentation of necrotizing fasciitis of the face, neck and anterior thoracic wall. Despite adverse prognostic indicators, surgical debridement was performed. Intensive medical treatment included continuous renal replacement therapy and intravenous immunoglobulin. Survival in this case illustrates that the window of opportunity for surgically treating CCNF extends to the advanced stages of the disease, albeit with increased morbidity.

Scarring in external dacryocystorhinostomy: fact or fiction?

PURPOSE

To determine patients' long-term satisfaction with external dacryocystorhinostomy (DCR) with respect to the visibility of the scar and the resolution of symptoms.

METHOD

A single postal questionnaire with stamped addressed envelope for reply was sent to 204 sequential external primary DCR patients operated on by AAM from January 1999 to April 2002.

RESULTS

Of the 79% who replied, 67% rated the scar as invisible with 97% happy with the scar. In 92% the epiphora was either improved or cured and 85% would recommend the operation. Younger patients were significantly more likely to rate the scar as visible but equally likely to rate the scar as good or better. Women were no more likely than men to rate the scar as visible, but if visible, were more likely to consider the scar poor.

CONCLUSIONS

There was an excellent response rate for a single questionnaire. Patient satisfaction with the DCR scar is very high, with the majority considering the scar invisible. Only 3% remained unhappy with the scar. Overall patient satisfaction with external DCR is very high, for the majority of patients the procedure is effective, and 85% would recommend the operation.