Cyanobacterial ultrastructure in light of genomic sequence data.

Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.

Prognostic role of FGFR1 amplification in early-stage non-small cell lung cancer.

BACKGROUND: Recently, fibroblast growth factor receptor 1 (FGFR1) was discovered in squamous cell carcinomas (SCC) of the lung with FGFR1 amplification described as a promising predictive marker for anti-FGFR inhibitor treatment. Only few data are available regarding prevalence, prognostic significance and clinico-pathological characteristics of FGFR1-amplified and early-stage non-small cell lung carcinomas (NSCLC). We therefore investigated the FGFR1 gene status in a large number of well-characterised early-stage NSCLC. METHODS: FGFR1 gene status was evaluated using a commercially available fluorescent in situ hybridisation (FISH) probe on a tissue microarray (TMA). This TMA harbours 329 resected, formalin-fixed and paraffin-embedded, nodal-negative NSCLC with a UICC stage I-II. The FISH results were correlated with clinico-pathological features and overall survival (OS). RESULTS: The prevalence of an FGFR1 amplification was 12.5% (41/329) and was significantly (P<0.0001) higher in squamous cell carcinoma (SCC) (20.7%) than in adenocarcinoma (2.2%) and large cell carcinoma (13%). Multivariate analysis revealed significantly (P=0.0367) worse 5-year OS in patients with an FGFR1-amplified NSCLC. CONCLUSIONS: FGFR1 amplification is common in early-stage SCC of the lung and is an independent and adverse prognostic marker. Its potential role as a predictive marker for targeted therapies or adjuvant treatment needs further investigation.

Molecular approaches for monitoring potentially toxic marine and freshwater phytoplankton species.

Harmful phytoplankton species are a growing problem in freshwater and marine ecosystems, because of their ability to synthesize toxins that threaten both animal and human health. The monitoring of these microorganisms has so far been based on conventional methods, mainly involving the microscopic counting and identification of cells, and using analytical and bioanalytical methods to identify and quantify the toxins. However, the increasing number of microbial sequences in the GeneBank database and the development of new tools in the last 15 years nowadays enables the use of molecular methods for detection and quantification of harmful phytoplankton species and their toxins. These methods provide species-level identification of the microorganisms of interest, and their early detection in the environment by PCR techniques. Moreover, real time PCR can be used to quantify the cells of interest, and in some cases to evaluate the proportion of toxin-producing and non-toxin-producing genotypes in a population. Recently, microarray technologies have also been used to achieve simultaneous detection and semi-quantification of harmful species in environmental samples. These methods look very promising, but so far their use remains limited to research. The need for validation for routine use and the cost of these methods still hamper their use in monitoring programs.

Acute respiratory distress syndrome secondary to antisynthetase syndrome is reversible with tacrolimus.

Polymyositis and interstitial lung diseases, predominantly nonspecific interstitial pneumonia (NSIP), are known to be frequent in antisynthetase syndrome, where anti-aminoacyl-tRNA synthetase antibodies are often identified. An unusual case of acute respiratory distress syndrome, secondary to such proven NSIP of cellular type with predominant CD8 lymphocytes, is described herein. The patient described in the present case study initially had a poor recovery with high dose of steroids, but this was followed by a good improvement after the prescription of tacrolimus and a low dose of prednisone. A precise diagnosis in similar circumstances may be life-saving, allowing the successful application of new immunosuppressants.

Origin and prognostic value of circulating KRAS mutations in lung cancer patients.

Because of the current controversy on the origin and clinical value of circulating KRAS codon 12 mutations in lung cancer, we screened 180 patients using a combined restriction fragment-length polymorphism and polymerase chain reaction (RFLP-PCR) assay. We detected KRAS mutations in 9% plasma samples and 0% matched lymphocytes. Plasma KRAS mutations correlated significantly with poor prognosis. We validated the positive results in a second laboratory by DNA sequencing and found matching codon 12 sequences in blood and tumor in 78% evaluable cases. These results support the notion that circulating KRAS mutations originate from tumors and are prognostically relevant in lung cancer.

Role of cyanobacteria in the biodegradation of crude oil by a tropical cyanobacterial mat.

Cyanobacterial mats are ubiquitous in tropical petroleum-polluted environments. They form a high biodiversity microbial consortium that contains efficient hydrocarbons degraders. A cyanobacterial mat collected from a petroleum-contaminated environment located in Indonesia was studied for its biodegradation potential. In the field, the natural mat was shown to degrade efficiently the crude oil present in the environment. This natural mat demonstrated also a strong activity of degradation on model crude oil under laboratory conditions. In axenic cultures, the monospecific cyanobacterium Phormidium animale that constitute the bulk of the biomass did not exhibit any degradative capacity on hydrocarbons in the range of C13-C35 carbon atom number either in autotrophic or heterotrophic conditions. It was concluded that this cyanobacterial strain living on a heavily contaminated site had no direct effect on biodegradation of crude oil, the degradation activity being exclusively achieved by the other microorganisms present in the microbial consortium of the mat.

Y(1)-mediated effect of neuropeptide Y in cancer: breast carcinomas as targets.

Overexpression of selected peptide receptors in human tumors has been shown to represent clinically relevant targets for cancer diagnosis and therapy. Neuropeptide Y (NPY) is a peptide neurotransmitter mediating feeding behavior and vasoconstriction. It has never been shown to be involved in human cancer. We show here, using in vitro receptor autoradiography, a NPY receptor incidence of 85% in primary human breast carcinomas (n = 95) and of 100% in lymph node metastases of receptor-positive primaries (n = 27), predominantly as Y(1) subtype, whereas non-neoplastic human breast expressed Y(2) preferentially. Y(1) mRNA was detected in Y(1)-expressing tumors by in situ hybridization, whereas Y(2) mRNA was found in normal breast tissue. The strong predominance of Y(1) in breast carcinomas compared with Y(2) in normal breast suggests that neoplastic transformation can switch the NPY receptor expression from Y(2) to Y(1) subtype. Moreover, in Y(1)-expressing human SK-N-MC tumor cells, an NPY-induced, dose-dependent inhibition of tumor cell growth of >40% was observed, suggesting a functional role of NPY in cancer, mediated by Y(1). NPY should therefore be added to the list of small regulatory peptides related to cancer. The high incidence of Y(1) in in situ, invasive, and metastatic breast cancers allows for the possibility to target them for diagnosis and therapy with NPY analogues.

Cyclin D1 overexpression in bronchial epithelia of patients with lung cancer is associated with smoking and predicts survival.

PURPOSE: Cyclin D1 is overexpressed in almost 60% of resectable non-small-cell lung cancer (NSCLC). In the absence of cyclin D1 gene amplification, overexpression is characterized by allelic imbalanced transcript levels. METHODS: The aims were to study cyclin D1 expression by immunohistochemistry and allelic balance of transcripts in tumor-free bronchial epithelia from patients with resectable NSCLC by using monoclonal antibodies (48 patients and 288 sites), microdissection/reverse transcriptase polymerase chain reaction/restriction fragment length polymorphism analyses (24 patients and 144 sites). Derived data were related to patient characteristics-in particular, smoking habits. RESULTS: In 167 (58%) of 288 sites, cyclin D1 was overexpressed, with cytoplasmic and nuclear sublocalization in 53% and 7% of all sites, respectively. Nuclear overexpression was more frequent in premalignant versus normal or hyperplastic epithelia (55% v 3%; P <.0001). Allele-specific expression imbalances were found in 69 (48%) of 144 sites; in particular, those in which cyclin D1 was overexpressed (P =.004). In 14 (58%) of 24 patients, balanced or imbalanced transcript ratios and degree of expression were consistent at all sites for the same patient, whereas in another 10 patients, transcript balances and cyclin D1 expression patterns varied across the sites. Nuclear cyclin D1 expression in at least one site (14 of 48 patients) was linked to heavy smoking (> 40 pack-years; P =.02) and shorter overall survival (P =.01). CONCLUSION: Allele-specific, probably damage-driven, deregulation of the cyclin D1 gene may precede and perhaps facilitate the spread of preneoplastic clones across the bronchial epithelial surface in a significant number of patients. Cyclin D1 expression at multiple bronchial sites may identify a subgroup of heavy-smoking patients with poor outcome.

Pre-eclampsia with acute heart failure postpartum as primary manifestation of systemic lupus erythematosus.

Pre-eclampsia occurs in 2-5% of pregnancies of healthy women. Here, we present a rare case of pre-eclampsia with overt acute heart failure, which was the primary manifestation of systemic lupus erythematosus with cardiac and renal involvement.

Video thoracoscopic surgery used to manage tuberculosis in thoracic surgery.

BACKGROUND: The aim of this study was to evaluate the indications and results of video-assisted thoracic surgery (VATS) for the management of tuberculosis in 10 patients with unusual clinical and radiologic presentation for the disease. METHODS: From March 2000 to March 2002, 96 diagnostic VATS operations for unclear thoracic lesions were performed at the authors' institution. Their final diagnosis for 10 (10.4%) of these patients was tuberculosis. The suspected preoperative diagnoses were pancoast tumour (n = 1), pericardial effusion (n = 1), pleural mesothelioma (n = 1), pleural empyema (n = 2), mediastinal lymphoma (n = l), and lung cancer (n = 4). RESULTS: For all the patients, the diagnosis of tuberculosis was achieved by VATS. The duration of drainage was 2.5 days. There have been neither morbidity nor mortality since surgery. The hospital stay was 3 to 5 days. CONCLUSION: Thoracoscopy is a safe and effective procedure for the management of tuberculosis. Tuberculosis should be kept in mind during the differential diagnosis of unknown thoracic lesions, and also for patients who live in economically well developed countries and are not immune compromised.

[Acute dyspnea--what should I not forget?]. / Akute Dyspnoe--was darf ich nicht vergessen?

Acute dyspnea represents a diagnostic challenge even for the experienced physician. There are no prospectively evaluated diagnostic algorithms dealing with this frequent clinical problem. First of all, the emergency has to be assessed and life supporting measures have to be considered. In addition to a thorough medical history and clinical examination, chest X-ray, spirometry, ECG, hemoglobin measurement, BNP and D-dimer testing represent valuable diagnostic tools and are available to GP's. Most commonly, acute dyspnoea is pulmonary or cardiac in origin. Up to one third of all cases will have several causes. Functional dyspnea is difficult to diagnose but should be taken into consideration after excluding any somatic cause. Hyperventilation is found in both, organic and non organic diseases, and is therefore an inappropriate criterion to differentiate between the two. The mainstay in the management of any symptom is to primarily treat the underlying disease. A significant hypoxemia (SO2 < 90%, pO2 < 60 mmHg) ought to be corrected by supplemental oxygen. It is inappropriate to withhold oxygen from patients with COPD and severe hypoxemia just to avoid hypercapnia. Besides oxygen, opiates efficiently relief dyspnoea but harbour the risk of respiratory depression, altered mental status or aspiration.

Effects of the calcium antagonist tiapamil on pulmonary gas exchange in patients with chronic obstructive pulmonary disease who receive salbutamol.

Patients with chronic obstructive pulmonary disease (COPD) and cardiovascular diseases are frequently given combination therapy with a beta 2-agonist and a calcium antagonist. Each drug is known to increase ventilation-perfusion inequalities. It was our aim to define the effects of their combination on lung function and on pulmonary gas exchange in eight subjects with COPD but partially reversible airway obstruction. Sixty minutes after placebo or 450 mg tiapamil, subjects inhaled 0.2 mg salbutamol. There was no significant effect of tiapamil on specific airway conductance and the forced expiratory volume in 1 second before or after the inhalation of salbutamol. Blood was drawn 30, 55, 80, and 100 minutes after placebo or tiapamil dosing. After placebo the mean (+/- SD) arterial oxygen tension (Pao2) fell from 67.1 +/- 7.3 to 64.4 +/- 5.5 mm Hg and the mean alveolar-arterial oxygen tension difference (AaDo2) rose from 34.6 +/- 8.4 to 40.5 +/- 6.8 mm Hg. After tiapamil the mean Pao2 fell from 68.7 +/- 7.3 to 66.4 +/- 5.8 mm Hg and the mean AaDo2 rose from 35.1 +/- 6.8 to 38.7 +/- 7.4 mm Hg. The changes in Pao2 were not significant. The increase in AaDo2 after placebo was significant, but that after tiapamil was not. We conclude that the combination of the calcium antagonist tiapamil and the bronchodilator salbutamol is safe with respect to lung function in COPD. There is no evidence that tiapamil increases beta 2-agonist-induced impairment in pulmonary gas exchange.

Sleepiness-related accidents in sleep apnea patients.

The frequency of motor vehicle and working accidents was analyzed by means of a strictly anonymous questionnaire in 156 patients with sleep apnea syndrome (SAS) and in 160 age-gender matched controls. In the SAS group 12.4% of all drivers had motor vehicle accidents as compared to 2.9% in the control group (p<0.005). The motor vehicle accident rate was 13.0 per million km in patients with more severe SAS (AHI > 34/h, n=78) as compared to 1.1 in patients with milder SAS (AHI 10-34/h, n=78) (p<0.05), and 0.78 in control group (p<0.005), respectively. The accident rates in both patients and the control group were also greater than the rate of 0.02 "accidents due to sleepiness" per one million km in the Swiss driving population as reported by official statistics. During treatment with nasal continuous airway pressure (nCPAP) in 85 SAS patients, the motor vehicle accident rate dropped from 10.6 to 2.7 per million km (p<0.05). We conclude that patients with moderate to severe SAS have an up to fifteen-fold risk increase of motor vehicle accidents that constitutes a serious and often underestimated hazard on the roads, which can be reduced by adequate treatment.

Alterations of cell cycle regulators are less frequent in advanced non-small cell lung cancer than in resectable tumours.

Prognosis of lung cancer is related to stage of disease at time of diagnosis. In this study we examine alterations of pathways governing the cell cycle, in particular pRb-cyclinD1-p16 alpha and p53-p14ARF, in a series of NSCLC (n=92) at different stages at diagnosis. Using immunohistochemistry, we assessed the expression of the retinoblastoma protein (pRb), cyclin D1, p16 alpha, p53 and p14ARF. Tumours in stage I-IIIA (resectable) were more likely to have alterations in the pRb-cyclinD1-p16 alpha pathway than tumours in advanced stage (IIIB-IV) (90% versus 63%, P=0.002). pRb and p14ARF were more frequently downregulated in resectable tumours (P< or =0.03), and cyclin D1, p16 alpha, and p53 were altered at a similar frequency in resectable and advanced tumours. In 12 patients, metastatic sites (5 lymph node, 3 bone, 2 brain and 2 gastrointestinal metastases) were available for comparison with the primary tumour: 19 altered protein expressions were found to be concordant, six additional alterations (in 4 patients) were found in the metastases only, especially in lymph node metastases (3 patients). Compared with normal protein expression, both pathway alterations were associated with a longer survival (P=0.02). In a multivariate analysis (Cox regression) this difference was not maintained after adjustment for age, stage and tumour differentiation. Cyclin D1 was the sole protein with independent prognostic value in resectable tumours: the relative risk of local relapse was 4.7 in tumours without cyclin D1 overexpression (P=0.02, Cox regression analysis). No protein studied had a predictive significance for response after chemotherapy in non-resectable tumours. These results demonstrate a strong correlation between stage and pathway alterations, cell cycle regulators being less likely altered in advanced NSCLC. Tumours with defects in these control pathways tend therefore to remain localised and to metastasize at a later phase in tumour development. This finding might be an explanation for distinct biological behaviour (e.g. chemotherapy response) of resectable versus advanced disease.

Immunohistochemical localization of somatostatin receptor sst2A in human gut and lung tissue: possible implications for physiology and carcinogenesis.

Many neuroendocrine gastrointestinal and lung tumors express sst2A somatostatin receptors. Because the cellular location of sst2A in the corresponding non-neoplastic tissue is unknown, we searched for sst2A immuno-reactive cells and characterized their type in these tissues using a highly specific sst2A antibody (R2-88). Epithelial sst2A cells, identified as neuroendocrine, gastrin-producing cells, were found in large numbers in the antrum and the duodenum, but not in the gastric corpus. They were also present in the proximal jejunum, rarely noted in the distal jejunum and ileum, and absent in the large intestine and the appendix vermiformis. Moreover, sst2A cells were found abundantly in the neural plexus. sst2A receptors on antral gastrin cells could mediate somatostatin inhibition on gastrin secretion, whereas those in the neural plexus could mediate somatostatin effects on motility and ion transport in the lower gastrointestinal tract. Rare sst2A cells in bronchi and bronchioles located basally and parabasally in the gastrointestinal epithelium were detected that could represent stem/progenitor cells. It is currently not clear whether and which of the identified sst2A cells are at the origin of sst2A-positive neuroendocrine gut or lung tumors.

Low plasma concentrations of ionized calcium in patients with asthma.

It has been suggested that calcium homeostasis is abnormal in the vascular smooth muscle of hypertensive patients and in the bronchial smooth muscle in asthmatics. We have found the mean baseline concentration of plasma ionized calcium to be significantly lower both in 12 asthmatics with exercise-induced asthma (EIA) [1.16 +/- 0.01 (SE) mmol/l, P less than 0.001] and in 20 asthmatics without EIA (1.16 +/- 0.01; P less than 0.001) compared with 42 healthy subjects (1.24 +/- 0.01). The mean concentrations of plasma ionized calcium were not significantly different in asthmatics with and without EIA when measured either before treadmill exercise, during the last seconds of this exercise, or 10 or 20 min after exercise but were significantly lower than in another seven healthy subjects who undertook the same exercise protocol. Total plasma calcium concentrations in the three exercising groups were not significantly different at any point in time. The results suggest that in bronchial asthma an alteration of calcium metabolism may be important, but they also suggest that there is no simple relationship between the plasma ionized calcium concentration and acute exercise-induced bronchoconstriction.

Accuracy of respiratory inductive plethysmograph in measuring tidal volume during sleep.

Respiratory inductance plethysmography (RIP) has been widely used to measure ventilation during sleep, but its accuracy in this role has not been adequately tested. We have thus examined the accuracy of the RIP by comparing tidal volume measured with RIP with that measured by a pneumotachograph in eight unrestrained normal subjects during sleep. We have also studied the effect of posture on the accuracy of the RIP. In all sleep stages the correlation between RIP tidal volume measurements and expired volume showed relatively poor correlations (mean r = 0.49-0.60), and the bias of the measurements varied widely. Changes in posture altered the correlations between the two measurements, with no systematic differences between positions. When the subjects resumed a position, the 95% confidence intervals of tidal volume measurement did not overlap the original confidence limits in that posture on 13 of 25 occasions. This study shows that the RIP does not accurately measure tidal volume during sleep in unrestrained subjects and should only be used for semiquantitative assessment of ventilation during sleep.

Functional assessment of chest wall integrity after methylmethacrylate reconstruction.

BACKGROUND: All patients with extensive resection of the anterolateral chest wall and the sternum followed by reconstruction with methylmethacrylate substitutes were assessed prospectively 6 months after the operation to delineate chest wall integrity with pulmonary function and cine-magnetic resonance imaging. METHODS: Twenty-six patients underwent chest wall reconstruction by use of methylmethacrylate between 1994 and 1998 due to primary tumors in 35%, metastases in 27%, T3 lung cancer in 19%, and debridement for radionecrosis and osteomyelitis in 19% of patients. Three to eight ribs were resected and additional sternum resection was performed in 39% of patients. RESULTS: There was no 30-day mortality. All patients were extubated after the operation without need for reintubation. Prosthesis dislocation occurred in 1 patient and infection in 2 patients during follow-up. Nineteen patients (73%) suffered no restrictions of daily activities. Clinical examination revealed normal shoulder girdle function in 77% of patients. There was no significant difference between preoperative and postoperative FEV1 (forced expiratory volume in 1 second) measurements in patients with lobectomy or wedge resections. Cinemagnetic resonance imaging revealed concordant chest wall movements during respiration in 92% of patients without paradoxical movements or implant dislocations being observed. CONCLUSIONS: Large defects of the anterolateral chest wall and sternum can be reconstructed efficiently with methylmethacrylate substitutes with minimal morbidity and excellent cosmetic and functional outcome.

Video-assisted thoracoscopic surgery for fibrinopurulent pleural empyema in 67 patients.

BACKGROUND: The roles of different drainage procedures in the management of empyema have to be redefined now that video-assisted thoracoscopic surgery (VATS) has been introduced. The debridement of fibrinopurulent stage II empyema with the use of VATS was assessed prospectively in regard to control of infection and restoration of pulmonary function. METHODS: Between January 1992 and May 1996, all patients at our institution with fibrinopurulent empyema that did not respond to chest tube drainage and antibiotic therapy were treated by debridement with the use of VATS. The patients were followed up prospectively by clinical and radiologic assessments 3 and 6 months after the operation and by spirometry 6 months after the operation. RESULTS: Video-assisted thoracoscopic surgery was initiated in 67 patients, but conversion to open decortication was required because of the finding of advanced disease in 19 patients (28%). Forty-eight patients underwent successful debridement with the use of VATS. The mean operative time was 82.1 minutes (range, 50 to 135 minutes), the mean duration of postoperative chest tube placement was 4.1 days (range, 2 to 8 days), and the mean duration of postoperative hospitalization was 12.3 days (range, 4 to 42 days). No wound infections were observed during the postoperative course. Both the 30-day mortality rate and the recurrence (ie, need for thoracotomy) rate were 4%. The mean predicted vital capacity was 84.8% +/- 14.9% and the mean predicted forced expiratory volume in 1 second was 88.6% +/- 19.2% 6 months after the operation. CONCLUSIONS: Debridement with the use of VATS is safe and efficient for stage II empyema, but open decortication should be used for more advanced disease.